diff --git a/404.html b/404.html index 543fbf79..b588b409 100644 --- a/404.html +++ b/404.html @@ -9,7 +9,7 @@ - + diff --git a/ArgolightBDataset/index.html b/ArgolightBDataset/index.html deleted file mode 100644 index b4bc4888..00000000 --- a/ArgolightBDataset/index.html +++ /dev/null @@ -1,568 +0,0 @@ - - - - - - - - - - -Class: ArgolightBDataset - microscopemetrics-schema - - - - - - - - - - - -
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Class: ArgolightBDataset

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An Argolight sample pattern B dataset. This pattern consists of an array of circles

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URI: microscopemetrics_schema:ArgolightBDataset

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classDiagram - class ArgolightBDataset - MetricsDataset <|-- ArgolightBDataset - - ArgolightBDataset : acquisition_datetime - - ArgolightBDataset : data_reference - - ArgolightBDataset --> DataReference : data_reference - - ArgolightBDataset : description - - ArgolightBDataset : experimenter - - ArgolightBDataset --> Experimenter : experimenter - - ArgolightBDataset : input - - ArgolightBDataset --> ArgolightBInput : input - - ArgolightBDataset : linked_references - - ArgolightBDataset --> DataReference : linked_references - - ArgolightBDataset : microscope - - ArgolightBDataset --> Microscope : microscope - - ArgolightBDataset : name - - ArgolightBDataset : output - - ArgolightBDataset --> ArgolightBOutput : output - - ArgolightBDataset : processed - - ArgolightBDataset : sample - - ArgolightBDataset --> Sample : sample - - -
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Inheritance

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Slots

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NameCardinality and RangeDescriptionInheritance
input0..1
ArgolightBInput		direct
output0..1
ArgolightBOutput		direct
microscope1..1
Microscope		The microscope that was used to acquire the datasetMetricsDataset
sample0..1
Sample		The sample that was imagedMetricsDataset
experimenter0..1
Experimenter		The experimenter that performed the imaging experimentMetricsDataset
acquisition_datetime0..1
datetime		The datetime of the acquisitionMetricsDataset
processed1..1
Boolean		Has the dataset been processed by microscope-metricsMetricsDataset
data_reference0..1
DataReference		A reference to the dataMetricsObject
linked_references0..*
DataReference		A list of linked referencesMetricsObject
name0..1
String		The human readable name of an entityNamedObject
description0..1
String		A human readable description of an entityNamedObject
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Identifier and Mapping Information

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Schema Source

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  • from schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
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Mappings

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Mapping TypeMapped Value
selfmicroscopemetrics_schema:ArgolightBDataset
nativemicroscopemetrics_schema:ArgolightBDataset
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LinkML Source

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Direct

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name: ArgolightBDataset
-description: An Argolight sample pattern B dataset. This pattern consists of an array
-  of circles
-from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: MetricsDataset
-attributes:
-  input:
-    name: input
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    domain_of:
-    - MetricsDataset
-    - FieldIlluminationDataset
-    - PSFBeadsDataset
-    - ArgolightBDataset
-    - ArgolightEDataset
-    range: ArgolightBInput
-  output:
-    name: output
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    domain_of:
-    - MetricsDataset
-    - FieldIlluminationDataset
-    - PSFBeadsDataset
-    - ArgolightBDataset
-    - ArgolightEDataset
-    range: ArgolightBOutput
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Induced

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-
name: ArgolightBDataset
-description: An Argolight sample pattern B dataset. This pattern consists of an array
-  of circles
-from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: MetricsDataset
-attributes:
-  input:
-    name: input
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    alias: input
-    owner: ArgolightBDataset
-    domain_of:
-    - MetricsDataset
-    - FieldIlluminationDataset
-    - PSFBeadsDataset
-    - ArgolightBDataset
-    - ArgolightEDataset
-    range: ArgolightBInput
-  output:
-    name: output
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    alias: output
-    owner: ArgolightBDataset
-    domain_of:
-    - MetricsDataset
-    - FieldIlluminationDataset
-    - PSFBeadsDataset
-    - ArgolightBDataset
-    - ArgolightEDataset
-    range: ArgolightBOutput
-  microscope:
-    name: microscope
-    description: The microscope that was used to acquire the dataset
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: microscope
-    owner: ArgolightBDataset
-    domain_of:
-    - MetricsDataset
-    range: Microscope
-    required: true
-  sample:
-    name: sample
-    description: The sample that was imaged
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: sample
-    owner: ArgolightBDataset
-    domain_of:
-    - MetricsDataset
-    range: Sample
-  experimenter:
-    name: experimenter
-    description: The experimenter that performed the imaging experiment
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: experimenter
-    owner: ArgolightBDataset
-    domain_of:
-    - MetricsDataset
-    range: Experimenter
-  acquisition_datetime:
-    name: acquisition_datetime
-    description: The datetime of the acquisition
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: acquisition_datetime
-    owner: ArgolightBDataset
-    domain_of:
-    - MetricsDataset
-    - Image
-    range: datetime
-  processed:
-    name: processed
-    description: Has the dataset been processed by microscope-metrics
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    ifabsent: 'False'
-    alias: processed
-    owner: ArgolightBDataset
-    domain_of:
-    - MetricsDataset
-    range: boolean
-    required: true
-  data_reference:
-    name: data_reference
-    description: A reference to the data
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: data_reference
-    owner: ArgolightBDataset
-    domain_of:
-    - MetricsObject
-    range: DataReference
-    required: false
-  linked_references:
-    name: linked_references
-    description: A list of linked references
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: linked_references
-    owner: ArgolightBDataset
-    domain_of:
-    - MetricsObject
-    range: DataReference
-    required: false
-    inlined: true
-    inlined_as_list: true
-  name:
-    name: name
-    description: The human readable name of an entity
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: false
-    alias: name
-    owner: ArgolightBDataset
-    domain_of:
-    - NamedObject
-    - Experimenter
-    range: string
-    required: false
-  description:
-    name: description
-    description: A human readable description of an entity
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: false
-    alias: description
-    owner: ArgolightBDataset
-    domain_of:
-    - NamedObject
-    - Tag
-    range: string
-    required: false
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Class: ArgolightBDistanceKeyValues

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URI: microscopemetrics_schema:ArgolightBDistanceKeyValues

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classDiagram - class ArgolightBDistanceKeyValues - KeyValues <|-- ArgolightBDistanceKeyValues - - ArgolightBDistanceKeyValues : channel_A - - ArgolightBDistanceKeyValues : channel_B - - ArgolightBDistanceKeyValues : data_reference - - ArgolightBDistanceKeyValues --> DataReference : data_reference - - ArgolightBDistanceKeyValues : description - - ArgolightBDistanceKeyValues : linked_references - - ArgolightBDistanceKeyValues --> DataReference : linked_references - - ArgolightBDistanceKeyValues : mad_3d_dist - - ArgolightBDistanceKeyValues : mad_z_dist - - ArgolightBDistanceKeyValues : mean_3d_dist - - ArgolightBDistanceKeyValues : mean_z_dist - - ArgolightBDistanceKeyValues : median_3d_dist - - ArgolightBDistanceKeyValues : median_z_dist - - ArgolightBDistanceKeyValues : name - - ArgolightBDistanceKeyValues : std_3d_dist - - ArgolightBDistanceKeyValues : std_z_dist - - -
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Inheritance

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Slots

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NameCardinality and RangeDescriptionInheritance
channel_A0..*
Integer		The first channel number to which the measurements applydirect
channel_B0..*
Integer		The second channel number to which the measurements applydirect
mean_3d_dist0..*
Float		Mean of the 3D distances between spots for each permutation of channel A and ...direct
median_3d_dist0..*
Float		Median of the 3D distances between spots for each permutation of channel A an...direct
std_3d_dist0..*
Float		Standard deviation of the 3D distances between spots for each permutation of ...direct
mad_3d_dist0..*
Float		Median absolute deviation of the 3D distances between spots for each permutat...direct
mean_z_dist0..*
Float		Mean of the Z distances between spots for each permutation of channel A and Bdirect
median_z_dist0..*
Float		Median of the Z distances between spots for each permutation of channel A and...direct
std_z_dist0..*
Float		Standard deviation of the Z distances between spots for each permutation of c...direct
mad_z_dist0..*
Float		Median absolute deviation of the Z distances between spots for each permutati...direct
data_reference0..1
DataReference		A reference to the dataMetricsObject
linked_references0..*
DataReference		A list of linked referencesMetricsObject
name0..1
String		The human readable name of an entityNamedObject
description0..1
String		A human readable description of an entityNamedObject
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Usages

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used byused intypeused
ArgolightBOutputdistance_key_valuesrangeArgolightBDistanceKeyValues
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Identifier and Mapping Information

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Schema Source

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Mappings

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Mapping TypeMapped Value
selfmicroscopemetrics_schema:ArgolightBDistanceKeyValues
nativemicroscopemetrics_schema:ArgolightBDistanceKeyValues
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LinkML Source

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Direct

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name: ArgolightBDistanceKeyValues
-from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: KeyValues
-slots:
-- channel_A
-- channel_B
-- mean_3d_dist
-- median_3d_dist
-- std_3d_dist
-- mad_3d_dist
-- mean_z_dist
-- median_z_dist
-- std_z_dist
-- mad_z_dist
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Induced

-
-
name: ArgolightBDistanceKeyValues
-from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: KeyValues
-attributes:
-  channel_A:
-    name: channel_A
-    description: The first channel number to which the measurements apply
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    is_a: channel_nr
-    multivalued: true
-    alias: channel_A
-    owner: ArgolightBDistanceKeyValues
-    domain_of:
-    - ArgolightBDistanceKeyValues
-    range: integer
-  channel_B:
-    name: channel_B
-    description: The second channel number to which the measurements apply
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    is_a: channel_nr
-    multivalued: true
-    alias: channel_B
-    owner: ArgolightBDistanceKeyValues
-    domain_of:
-    - ArgolightBDistanceKeyValues
-    range: integer
-  mean_3d_dist:
-    name: mean_3d_dist
-    description: Mean of the 3D distances between spots for each permutation of channel
-      A and B
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: mean_3d_dist
-    owner: ArgolightBDistanceKeyValues
-    domain_of:
-    - ArgolightBDistanceKeyValues
-    range: float
-  median_3d_dist:
-    name: median_3d_dist
-    description: Median of the 3D distances between spots for each permutation of
-      channel A and B
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: median_3d_dist
-    owner: ArgolightBDistanceKeyValues
-    domain_of:
-    - ArgolightBDistanceKeyValues
-    range: float
-  std_3d_dist:
-    name: std_3d_dist
-    description: Standard deviation of the 3D distances between spots for each permutation
-      of channel A and B
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: std_3d_dist
-    owner: ArgolightBDistanceKeyValues
-    domain_of:
-    - ArgolightBDistanceKeyValues
-    range: float
-  mad_3d_dist:
-    name: mad_3d_dist
-    description: Median absolute deviation of the 3D distances between spots for each
-      permutation of channel A and B
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: mad_3d_dist
-    owner: ArgolightBDistanceKeyValues
-    domain_of:
-    - ArgolightBDistanceKeyValues
-    range: float
-  mean_z_dist:
-    name: mean_z_dist
-    description: Mean of the Z distances between spots for each permutation of channel
-      A and B
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: mean_z_dist
-    owner: ArgolightBDistanceKeyValues
-    domain_of:
-    - ArgolightBDistanceKeyValues
-    range: float
-  median_z_dist:
-    name: median_z_dist
-    description: Median of the Z distances between spots for each permutation of channel
-      A and B
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: median_z_dist
-    owner: ArgolightBDistanceKeyValues
-    domain_of:
-    - ArgolightBDistanceKeyValues
-    range: float
-  std_z_dist:
-    name: std_z_dist
-    description: Standard deviation of the Z distances between spots for each permutation
-      of channel A and B
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: std_z_dist
-    owner: ArgolightBDistanceKeyValues
-    domain_of:
-    - ArgolightBDistanceKeyValues
-    range: float
-  mad_z_dist:
-    name: mad_z_dist
-    description: Median absolute deviation of the Z distances between spots for each
-      permutation of channel A and B
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: mad_z_dist
-    owner: ArgolightBDistanceKeyValues
-    domain_of:
-    - ArgolightBDistanceKeyValues
-    range: float
-  data_reference:
-    name: data_reference
-    description: A reference to the data
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: data_reference
-    owner: ArgolightBDistanceKeyValues
-    domain_of:
-    - MetricsObject
-    range: DataReference
-    required: false
-  linked_references:
-    name: linked_references
-    description: A list of linked references
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: linked_references
-    owner: ArgolightBDistanceKeyValues
-    domain_of:
-    - MetricsObject
-    range: DataReference
-    required: false
-    inlined: true
-    inlined_as_list: true
-  name:
-    name: name
-    description: The human readable name of an entity
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: false
-    alias: name
-    owner: ArgolightBDistanceKeyValues
-    domain_of:
-    - NamedObject
-    - Experimenter
-    range: string
-    required: false
-  description:
-    name: description
-    description: A human readable description of an entity
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: false
-    alias: description
-    owner: ArgolightBDistanceKeyValues
-    domain_of:
-    - NamedObject
-    - Tag
-    range: string
-    required: false
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Class: ArgolightBInput

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URI: microscopemetrics_schema:ArgolightBInput

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classDiagram - class ArgolightBInput - MetricsInput <|-- ArgolightBInput - - ArgolightBInput : argolight_b_image - - ArgolightBInput --> Image : argolight_b_image - - ArgolightBInput : bit_depth - - ArgolightBInput : lower_threshold_correction_factors - - ArgolightBInput : remove_center_cross - - ArgolightBInput : saturation_threshold - - ArgolightBInput : sigma_x - - ArgolightBInput : sigma_y - - ArgolightBInput : sigma_z - - ArgolightBInput : spots_distance - - ArgolightBInput : upper_threshold_correction_factors - - -
-

Inheritance

- -

Slots

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
NameCardinality and RangeDescriptionInheritance
argolight_b_image1..1
Image		Input parameter: image of the argolight b pattern in the order TZYXCdirect
bit_depth0..1
Integer		Detector bit depthdirect
saturation_threshold1..1
Float		Tolerated saturation thresholddirect
spots_distance1..1
Float		Input parameter: distance between argolight spotsdirect
sigma_z1..1
Float		Smoothing factor for objects detection in the Z axisdirect
sigma_y1..1
Float		Smoothing factor for objects detection in the Y axisdirect
sigma_x1..1
Float		Smoothing factor for objects detection in the X axisdirect
lower_threshold_correction_factors0..*
Float		Input parameter: correction factor for the lower thresholdsdirect
upper_threshold_correction_factors0..*
Float		Input parameter: correction factor for the upper thresholdsdirect
remove_center_cross0..1
Boolean		Input parameter: remove the center cross found in some Argolight patternsdirect
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Usages

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used byused intypeused
ArgolightBDatasetinputrangeArgolightBInput
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Identifier and Mapping Information

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Schema Source

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  • from schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
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Mappings

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Mapping TypeMapped Value
selfmicroscopemetrics_schema:ArgolightBInput
nativemicroscopemetrics_schema:ArgolightBInput
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LinkML Source

- -

Direct

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name: ArgolightBInput
-from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: MetricsInput
-slots:
-- argolight_b_image
-- bit_depth
-- saturation_threshold
-- spots_distance
-- sigma_z
-- sigma_y
-- sigma_x
-- lower_threshold_correction_factors
-- upper_threshold_correction_factors
-- remove_center_cross
-slot_usage:
-  saturation_threshold:
-    name: saturation_threshold
-    domain_of:
-    - FieldIlluminationInput
-    - PSFBeadsInput
-    - ArgolightBInput
-    - ArgolightEInput
-    required: true
-  sigma_z:
-    name: sigma_z
-    description: Smoothing factor for objects detection in the Z axis
-    multivalued: false
-    ifabsent: float(1.0)
-    domain_of:
-    - PSFBeadsInput
-    - ArgolightBInput
-    required: true
-    minimum_value: 0.0
-    maximum_value: 5.0
-  sigma_y:
-    name: sigma_y
-    description: Smoothing factor for objects detection in the Y axis
-    multivalued: false
-    ifabsent: float(3.0)
-    domain_of:
-    - PSFBeadsInput
-    - ArgolightBInput
-    required: true
-    minimum_value: 0.0
-    maximum_value: 10.0
-  sigma_x:
-    name: sigma_x
-    description: Smoothing factor for objects detection in the X axis
-    multivalued: false
-    ifabsent: float(3.0)
-    domain_of:
-    - PSFBeadsInput
-    - ArgolightBInput
-    required: true
-    minimum_value: 0.0
-    maximum_value: 10.0
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Induced

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name: ArgolightBInput
-from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: MetricsInput
-slot_usage:
-  saturation_threshold:
-    name: saturation_threshold
-    domain_of:
-    - FieldIlluminationInput
-    - PSFBeadsInput
-    - ArgolightBInput
-    - ArgolightEInput
-    required: true
-  sigma_z:
-    name: sigma_z
-    description: Smoothing factor for objects detection in the Z axis
-    multivalued: false
-    ifabsent: float(1.0)
-    domain_of:
-    - PSFBeadsInput
-    - ArgolightBInput
-    required: true
-    minimum_value: 0.0
-    maximum_value: 5.0
-  sigma_y:
-    name: sigma_y
-    description: Smoothing factor for objects detection in the Y axis
-    multivalued: false
-    ifabsent: float(3.0)
-    domain_of:
-    - PSFBeadsInput
-    - ArgolightBInput
-    required: true
-    minimum_value: 0.0
-    maximum_value: 10.0
-  sigma_x:
-    name: sigma_x
-    description: Smoothing factor for objects detection in the X axis
-    multivalued: false
-    ifabsent: float(3.0)
-    domain_of:
-    - PSFBeadsInput
-    - ArgolightBInput
-    required: true
-    minimum_value: 0.0
-    maximum_value: 10.0
-attributes:
-  argolight_b_image:
-    name: argolight_b_image
-    description: 'Input parameter: image of the argolight b pattern in the order TZYXC'
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: false
-    alias: argolight_b_image
-    owner: ArgolightBInput
-    domain_of:
-    - ArgolightBInput
-    range: Image
-    required: true
-  bit_depth:
-    name: bit_depth
-    description: Detector bit depth
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: false
-    alias: bit_depth
-    owner: ArgolightBInput
-    domain_of:
-    - FieldIlluminationInput
-    - PSFBeadsInput
-    - ArgolightBInput
-    - ArgolightEInput
-    range: integer
-    minimum_value: 1
-    maximum_value: 64
-  saturation_threshold:
-    name: saturation_threshold
-    description: Tolerated saturation threshold. If the amount of saturated pixels
-      is above this threshold,  the image is considered as saturated and the analysis
-      is not performed.
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: false
-    ifabsent: float(0.01)
-    alias: saturation_threshold
-    owner: ArgolightBInput
-    domain_of:
-    - FieldIlluminationInput
-    - PSFBeadsInput
-    - ArgolightBInput
-    - ArgolightEInput
-    range: float
-    required: true
-    minimum_value: 0.0
-    maximum_value: 1.0
-  spots_distance:
-    name: spots_distance
-    description: 'Input parameter: distance between argolight spots'
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: false
-    alias: spots_distance
-    owner: ArgolightBInput
-    domain_of:
-    - ArgolightBInput
-    range: float
-    required: true
-  sigma_z:
-    name: sigma_z
-    description: Smoothing factor for objects detection in the Z axis
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: false
-    ifabsent: float(1.0)
-    alias: sigma_z
-    owner: ArgolightBInput
-    domain_of:
-    - PSFBeadsInput
-    - ArgolightBInput
-    range: float
-    required: true
-    minimum_value: 0.0
-    maximum_value: 5.0
-  sigma_y:
-    name: sigma_y
-    description: Smoothing factor for objects detection in the Y axis
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: false
-    ifabsent: float(3.0)
-    alias: sigma_y
-    owner: ArgolightBInput
-    domain_of:
-    - PSFBeadsInput
-    - ArgolightBInput
-    range: float
-    required: true
-    minimum_value: 0.0
-    maximum_value: 10.0
-  sigma_x:
-    name: sigma_x
-    description: Smoothing factor for objects detection in the X axis
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: false
-    ifabsent: float(3.0)
-    alias: sigma_x
-    owner: ArgolightBInput
-    domain_of:
-    - PSFBeadsInput
-    - ArgolightBInput
-    range: float
-    required: true
-    minimum_value: 0.0
-    maximum_value: 10.0
-  lower_threshold_correction_factors:
-    name: lower_threshold_correction_factors
-    description: 'Input parameter: correction factor for the lower thresholds.  Must
-      be a list with length equal to the number of channels or a single float if all
-      equal'
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: lower_threshold_correction_factors
-    owner: ArgolightBInput
-    domain_of:
-    - ArgolightBInput
-    range: float
-    required: false
-  upper_threshold_correction_factors:
-    name: upper_threshold_correction_factors
-    description: 'Input parameter: correction factor for the upper thresholds. Must
-      be a tuple with length equal to the number of channels or a single float if
-      all equal'
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: upper_threshold_correction_factors
-    owner: ArgolightBInput
-    domain_of:
-    - ArgolightBInput
-    range: float
-    required: false
-  remove_center_cross:
-    name: remove_center_cross
-    description: 'Input parameter: remove the center cross found in some Argolight
-      patterns'
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: false
-    ifabsent: 'False'
-    alias: remove_center_cross
-    owner: ArgolightBInput
-    domain_of:
-    - ArgolightBInput
-    range: boolean
-    required: false
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Class: ArgolightBIntensityKeyValues

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URI: microscopemetrics_schema:ArgolightBIntensityKeyValues

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classDiagram - class ArgolightBIntensityKeyValues - KeyValues <|-- ArgolightBIntensityKeyValues - - ArgolightBIntensityKeyValues : channel_nr - - ArgolightBIntensityKeyValues : data_reference - - ArgolightBIntensityKeyValues --> DataReference : data_reference - - ArgolightBIntensityKeyValues : description - - ArgolightBIntensityKeyValues : intensity_max_spot - - ArgolightBIntensityKeyValues : intensity_max_spot_roi - - ArgolightBIntensityKeyValues : intensity_min_spot - - ArgolightBIntensityKeyValues : intensity_min_spot_roi - - ArgolightBIntensityKeyValues : linked_references - - ArgolightBIntensityKeyValues --> DataReference : linked_references - - ArgolightBIntensityKeyValues : mad_mean_intensity - - ArgolightBIntensityKeyValues : mean_intensity - - ArgolightBIntensityKeyValues : median_intensity - - ArgolightBIntensityKeyValues : min_max_intensity_ratio - - ArgolightBIntensityKeyValues : name - - ArgolightBIntensityKeyValues : nr_of_spots - - ArgolightBIntensityKeyValues : std_mean_intensity - - -
-

Inheritance

- -

Slots

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
NameCardinality and RangeDescriptionInheritance
channel_nr0..*
Integer		The channel number to which the measurements applydirect
nr_of_spots0..*
Integer		Number of argolight spots detected for each channeldirect
intensity_max_spot0..*
Float		Integrated intensity of the most intense spot for each channeldirect
intensity_max_spot_roi0..*
Integer		ROI number of the most intense spot for each channeldirect
intensity_min_spot0..*
Float		Integrated intensity of the least intense spot for each channeldirect
intensity_min_spot_roi0..*
Integer		ROI number of the least intense spot for each channeldirect
mean_intensity0..*
Float		Mean of all spots integrated intensity for each channeldirect
median_intensity0..*
Float		Median of all spots integrated intensity for each channeldirect
std_mean_intensity0..*
Float		Standard deviation of all spots integrated intensity for each channeldirect
mad_mean_intensity0..*
Float		Median absolute deviation of all spots integrated intensity for each channeldirect
min_max_intensity_ratio0..*
Float		Ratio between the integrated intensities between the most intense and the lea...direct
data_reference0..1
DataReference		A reference to the dataMetricsObject
linked_references0..*
DataReference		A list of linked referencesMetricsObject
name0..1
String		The human readable name of an entityNamedObject
description0..1
String		A human readable description of an entityNamedObject
-

Usages

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used byused intypeused
ArgolightBOutputintensity_key_valuesrangeArgolightBIntensityKeyValues
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Identifier and Mapping Information

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Schema Source

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    -
  • from schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
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Mappings

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Mapping TypeMapped Value
selfmicroscopemetrics_schema:ArgolightBIntensityKeyValues
nativemicroscopemetrics_schema:ArgolightBIntensityKeyValues
-

LinkML Source

- -

Direct

-
-
name: ArgolightBIntensityKeyValues
-from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: KeyValues
-slots:
-- channel_nr
-- nr_of_spots
-- intensity_max_spot
-- intensity_max_spot_roi
-- intensity_min_spot
-- intensity_min_spot_roi
-- mean_intensity
-- median_intensity
-- std_mean_intensity
-- mad_mean_intensity
-- min_max_intensity_ratio
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-
-
-

Induced

-
-
name: ArgolightBIntensityKeyValues
-from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: KeyValues
-attributes:
-  channel_nr:
-    name: channel_nr
-    description: The channel number to which the measurements apply
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: channel_nr
-    owner: ArgolightBIntensityKeyValues
-    domain_of:
-    - PSFBeadsKeyValues
-    - ArgolightBIntensityKeyValues
-    - ArgolightEKeyValues
-    range: integer
-    minimum_value: 0
-  nr_of_spots:
-    name: nr_of_spots
-    description: Number of argolight spots detected for each channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: nr_of_spots
-    owner: ArgolightBIntensityKeyValues
-    domain_of:
-    - ArgolightBIntensityKeyValues
-    range: integer
-  intensity_max_spot:
-    name: intensity_max_spot
-    description: Integrated intensity of the most intense spot for each channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: intensity_max_spot
-    owner: ArgolightBIntensityKeyValues
-    domain_of:
-    - ArgolightBIntensityKeyValues
-    range: float
-  intensity_max_spot_roi:
-    name: intensity_max_spot_roi
-    description: ROI number of the most intense spot for each channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: intensity_max_spot_roi
-    owner: ArgolightBIntensityKeyValues
-    domain_of:
-    - ArgolightBIntensityKeyValues
-    range: integer
-  intensity_min_spot:
-    name: intensity_min_spot
-    description: Integrated intensity of the least intense spot for each channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: intensity_min_spot
-    owner: ArgolightBIntensityKeyValues
-    domain_of:
-    - ArgolightBIntensityKeyValues
-    range: float
-  intensity_min_spot_roi:
-    name: intensity_min_spot_roi
-    description: ROI number of the least intense spot for each channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: intensity_min_spot_roi
-    owner: ArgolightBIntensityKeyValues
-    domain_of:
-    - ArgolightBIntensityKeyValues
-    range: integer
-  mean_intensity:
-    name: mean_intensity
-    description: Mean of all spots integrated intensity for each channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: mean_intensity
-    owner: ArgolightBIntensityKeyValues
-    domain_of:
-    - ArgolightBIntensityKeyValues
-    range: float
-  median_intensity:
-    name: median_intensity
-    description: Median of all spots integrated intensity for each channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: median_intensity
-    owner: ArgolightBIntensityKeyValues
-    domain_of:
-    - ArgolightBIntensityKeyValues
-    range: float
-  std_mean_intensity:
-    name: std_mean_intensity
-    description: Standard deviation of all spots integrated intensity for each channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: std_mean_intensity
-    owner: ArgolightBIntensityKeyValues
-    domain_of:
-    - ArgolightBIntensityKeyValues
-    range: float
-  mad_mean_intensity:
-    name: mad_mean_intensity
-    description: Median absolute deviation of all spots integrated intensity for each
-      channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: mad_mean_intensity
-    owner: ArgolightBIntensityKeyValues
-    domain_of:
-    - ArgolightBIntensityKeyValues
-    range: float
-  min_max_intensity_ratio:
-    name: min_max_intensity_ratio
-    description: Ratio between the integrated intensities between the most intense
-      and the least intense spots for each channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: min_max_intensity_ratio
-    owner: ArgolightBIntensityKeyValues
-    domain_of:
-    - ArgolightBIntensityKeyValues
-    range: float
-  data_reference:
-    name: data_reference
-    description: A reference to the data
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: data_reference
-    owner: ArgolightBIntensityKeyValues
-    domain_of:
-    - MetricsObject
-    range: DataReference
-    required: false
-  linked_references:
-    name: linked_references
-    description: A list of linked references
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: linked_references
-    owner: ArgolightBIntensityKeyValues
-    domain_of:
-    - MetricsObject
-    range: DataReference
-    required: false
-    inlined: true
-    inlined_as_list: true
-  name:
-    name: name
-    description: The human readable name of an entity
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: false
-    alias: name
-    owner: ArgolightBIntensityKeyValues
-    domain_of:
-    - NamedObject
-    - Experimenter
-    range: string
-    required: false
-  description:
-    name: description
-    description: A human readable description of an entity
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: false
-    alias: description
-    owner: ArgolightBIntensityKeyValues
-    domain_of:
-    - NamedObject
-    - Tag
-    range: string
-    required: false
-
-
-
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- -
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- - - - \ No newline at end of file diff --git a/ArgolightBOutput/index.html b/ArgolightBOutput/index.html deleted file mode 100644 index 19903432..00000000 --- a/ArgolightBOutput/index.html +++ /dev/null @@ -1,682 +0,0 @@ - - - - - - - - - - -Class: ArgolightBOutput - microscopemetrics-schema - - - - - - - - - - - -
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Class: ArgolightBOutput

-

URI: microscopemetrics_schema:ArgolightBOutput

-
classDiagram - class ArgolightBOutput - MetricsOutput <|-- ArgolightBOutput - - ArgolightBOutput : comment - - ArgolightBOutput --> Comment : comment - - ArgolightBOutput : distance_key_values - - ArgolightBOutput --> ArgolightBDistanceKeyValues : distance_key_values - - ArgolightBOutput : errors - - ArgolightBOutput : intensity_key_values - - ArgolightBOutput --> ArgolightBIntensityKeyValues : intensity_key_values - - ArgolightBOutput : processing_application - - ArgolightBOutput : processing_datetime - - ArgolightBOutput : processing_entity - - ArgolightBOutput : processing_log - - ArgolightBOutput : processing_version - - ArgolightBOutput : spots_centers_of_mass - - ArgolightBOutput --> ArgolightBCentersOfMass : spots_centers_of_mass - - ArgolightBOutput : spots_distances - - ArgolightBOutput --> Table : spots_distances - - ArgolightBOutput : spots_labels_image - - ArgolightBOutput --> ImageMask : spots_labels_image - - ArgolightBOutput : spots_properties - - ArgolightBOutput --> Table : spots_properties - - ArgolightBOutput : warnings - - -
-

Inheritance

- -

Slots

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
NameCardinality and RangeDescriptionInheritance
spots_labels_image0..1
ImageMask		Labels image of the argolight segmented spots provided in the order TZYXCdirect
spots_centers_of_mass0..*
ArgolightBCentersOfMass		Centers of mass of the argolight spots provided as a list of ROIsdirect
intensity_key_values0..1
ArgolightBIntensityKeyValues		Key Intensity Measurements on Argolight spotsdirect
distance_key_values0..1
ArgolightBDistanceKeyValues		Key Distance Measurements on Argolight spotsdirect
spots_properties0..1
Table		Table of properties of the argolight spotsdirect
spots_distances0..1
Table		Table of distances between argolight spotsdirect
processing_application1..*
String		The application used to process the datasetMetricsOutput
processing_version1..*
String		The version of the application used to process the datasetMetricsOutput
processing_entity0..*
String		The entity that processed the datasetMetricsOutput
processing_datetime1..1
datetime		The datetime of the processing by microscope-metricsMetricsOutput
processing_log0..1
String		The log of the processing by microscope-metricsMetricsOutput
warnings0..*
String		The warnings of the processing by microscope-metricsMetricsOutput
errors0..*
String		The errors of the processing by microscope-metricsMetricsOutput
comment0..1
Comment		A human readable comment about the datasetMetricsOutput
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Usages

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used byused intypeused
ArgolightBDatasetoutputrangeArgolightBOutput
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Identifier and Mapping Information

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Schema Source

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  • from schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
    • -
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Mappings

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Mapping TypeMapped Value
selfmicroscopemetrics_schema:ArgolightBOutput
nativemicroscopemetrics_schema:ArgolightBOutput
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LinkML Source

- -

Direct

-
-
name: ArgolightBOutput
-from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: MetricsOutput
-attributes:
-  spots_labels_image:
-    name: spots_labels_image
-    description: Labels image of the argolight segmented spots provided in the order
-      TZYXC. Image intensities correspond to ROI labels
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    rank: 1000
-    multivalued: false
-    domain_of:
-    - ArgolightBOutput
-    range: ImageMask
-    required: false
-  spots_centers_of_mass:
-    name: spots_centers_of_mass
-    description: Centers of mass of the argolight spots provided as a list of ROIs.
-      One per channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    rank: 1000
-    multivalued: true
-    domain_of:
-    - ArgolightBOutput
-    range: ArgolightBCentersOfMass
-    required: false
-  intensity_key_values:
-    name: intensity_key_values
-    description: Key Intensity Measurements on Argolight spots
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    rank: 1000
-    multivalued: false
-    domain_of:
-    - ArgolightBOutput
-    range: ArgolightBIntensityKeyValues
-    required: false
-  distance_key_values:
-    name: distance_key_values
-    description: Key Distance Measurements on Argolight spots
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    rank: 1000
-    multivalued: false
-    domain_of:
-    - ArgolightBOutput
-    range: ArgolightBDistanceKeyValues
-    required: false
-  spots_properties:
-    name: spots_properties
-    description: Table of properties of the argolight spots
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    rank: 1000
-    multivalued: false
-    domain_of:
-    - ArgolightBOutput
-    range: Table
-    required: false
-  spots_distances:
-    name: spots_distances
-    description: Table of distances between argolight spots
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    rank: 1000
-    multivalued: false
-    domain_of:
-    - ArgolightBOutput
-    range: Table
-    required: false
-
-
-
-

Induced

-
-
name: ArgolightBOutput
-from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: MetricsOutput
-attributes:
-  spots_labels_image:
-    name: spots_labels_image
-    description: Labels image of the argolight segmented spots provided in the order
-      TZYXC. Image intensities correspond to ROI labels
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    rank: 1000
-    multivalued: false
-    alias: spots_labels_image
-    owner: ArgolightBOutput
-    domain_of:
-    - ArgolightBOutput
-    range: ImageMask
-    required: false
-  spots_centers_of_mass:
-    name: spots_centers_of_mass
-    description: Centers of mass of the argolight spots provided as a list of ROIs.
-      One per channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    rank: 1000
-    multivalued: true
-    alias: spots_centers_of_mass
-    owner: ArgolightBOutput
-    domain_of:
-    - ArgolightBOutput
-    range: ArgolightBCentersOfMass
-    required: false
-  intensity_key_values:
-    name: intensity_key_values
-    description: Key Intensity Measurements on Argolight spots
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    rank: 1000
-    multivalued: false
-    alias: intensity_key_values
-    owner: ArgolightBOutput
-    domain_of:
-    - ArgolightBOutput
-    range: ArgolightBIntensityKeyValues
-    required: false
-  distance_key_values:
-    name: distance_key_values
-    description: Key Distance Measurements on Argolight spots
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    rank: 1000
-    multivalued: false
-    alias: distance_key_values
-    owner: ArgolightBOutput
-    domain_of:
-    - ArgolightBOutput
-    range: ArgolightBDistanceKeyValues
-    required: false
-  spots_properties:
-    name: spots_properties
-    description: Table of properties of the argolight spots
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    rank: 1000
-    multivalued: false
-    alias: spots_properties
-    owner: ArgolightBOutput
-    domain_of:
-    - ArgolightBOutput
-    range: Table
-    required: false
-  spots_distances:
-    name: spots_distances
-    description: Table of distances between argolight spots
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    rank: 1000
-    multivalued: false
-    alias: spots_distances
-    owner: ArgolightBOutput
-    domain_of:
-    - ArgolightBOutput
-    range: Table
-    required: false
-  processing_application:
-    name: processing_application
-    description: The application used to process the dataset
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: processing_application
-    owner: ArgolightBOutput
-    domain_of:
-    - MetricsOutput
-    range: string
-    required: true
-  processing_version:
-    name: processing_version
-    description: The version of the application used to process the dataset
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: processing_version
-    owner: ArgolightBOutput
-    domain_of:
-    - MetricsOutput
-    range: string
-    required: true
-  processing_entity:
-    name: processing_entity
-    description: The entity that processed the dataset
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: processing_entity
-    owner: ArgolightBOutput
-    domain_of:
-    - MetricsOutput
-    range: string
-    required: false
-  processing_datetime:
-    name: processing_datetime
-    description: The datetime of the processing by microscope-metrics
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: processing_datetime
-    owner: ArgolightBOutput
-    domain_of:
-    - MetricsOutput
-    range: datetime
-    required: true
-  processing_log:
-    name: processing_log
-    description: The log of the processing by microscope-metrics
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: processing_log
-    owner: ArgolightBOutput
-    domain_of:
-    - MetricsOutput
-    range: string
-    required: false
-  warnings:
-    name: warnings
-    description: The warnings of the processing by microscope-metrics
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: warnings
-    owner: ArgolightBOutput
-    domain_of:
-    - MetricsOutput
-    range: string
-    required: false
-  errors:
-    name: errors
-    description: The errors of the processing by microscope-metrics
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: errors
-    owner: ArgolightBOutput
-    domain_of:
-    - MetricsOutput
-    range: string
-    required: false
-  comment:
-    name: comment
-    description: A human readable comment about the dataset
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: comment
-    owner: ArgolightBOutput
-    domain_of:
-    - MetricsOutput
-    range: Comment
-    required: false
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- - - - \ No newline at end of file diff --git a/ArgolightEDataset/index.html b/ArgolightEDataset/index.html deleted file mode 100644 index 623edbf3..00000000 --- a/ArgolightEDataset/index.html +++ /dev/null @@ -1,581 +0,0 @@ - - - - - - - - - - -Class: ArgolightEDataset - microscopemetrics-schema - - - - - - - - - - - -
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Class: ArgolightEDataset

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An Argolight sample pattern E dataset.

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It contains resolution data on the axis indicated:

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- axis 1 = Y resolution = lines along X axis

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- axis 2 = X resolution = lines along Y axis

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URI: microscopemetrics_schema:ArgolightEDataset

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classDiagram - class ArgolightEDataset - MetricsDataset <|-- ArgolightEDataset - - ArgolightEDataset : acquisition_datetime - - ArgolightEDataset : data_reference - - ArgolightEDataset --> DataReference : data_reference - - ArgolightEDataset : description - - ArgolightEDataset : experimenter - - ArgolightEDataset --> Experimenter : experimenter - - ArgolightEDataset : input - - ArgolightEDataset --> ArgolightEInput : input - - ArgolightEDataset : linked_references - - ArgolightEDataset --> DataReference : linked_references - - ArgolightEDataset : microscope - - ArgolightEDataset --> Microscope : microscope - - ArgolightEDataset : name - - ArgolightEDataset : output - - ArgolightEDataset --> ArgolightEOutput : output - - ArgolightEDataset : processed - - ArgolightEDataset : sample - - ArgolightEDataset --> Sample : sample - - -
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Inheritance

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Slots

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NameCardinality and RangeDescriptionInheritance
input0..1
ArgolightEInput		direct
output0..1
ArgolightEOutput		direct
microscope1..1
Microscope		The microscope that was used to acquire the datasetMetricsDataset
sample0..1
Sample		The sample that was imagedMetricsDataset
experimenter0..1
Experimenter		The experimenter that performed the imaging experimentMetricsDataset
acquisition_datetime0..1
datetime		The datetime of the acquisitionMetricsDataset
processed1..1
Boolean		Has the dataset been processed by microscope-metricsMetricsDataset
data_reference0..1
DataReference		A reference to the dataMetricsObject
linked_references0..*
DataReference		A list of linked referencesMetricsObject
name0..1
String		The human readable name of an entityNamedObject
description0..1
String		A human readable description of an entityNamedObject
-

Identifier and Mapping Information

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Schema Source

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  • from schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
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Mappings

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Mapping TypeMapped Value
selfmicroscopemetrics_schema:ArgolightEDataset
nativemicroscopemetrics_schema:ArgolightEDataset
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LinkML Source

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Direct

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name: ArgolightEDataset
-description: 'An Argolight sample pattern E dataset.
-
-  It contains resolution data on the axis indicated:
-
-  - axis 1 = Y resolution = lines along X axis
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-  - axis 2 = X resolution = lines along Y axis'
-from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: MetricsDataset
-attributes:
-  input:
-    name: input
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    domain_of:
-    - MetricsDataset
-    - FieldIlluminationDataset
-    - PSFBeadsDataset
-    - ArgolightBDataset
-    - ArgolightEDataset
-    range: ArgolightEInput
-  output:
-    name: output
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    domain_of:
-    - MetricsDataset
-    - FieldIlluminationDataset
-    - PSFBeadsDataset
-    - ArgolightBDataset
-    - ArgolightEDataset
-    range: ArgolightEOutput
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-
-
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Induced

-
-
name: ArgolightEDataset
-description: 'An Argolight sample pattern E dataset.
-
-  It contains resolution data on the axis indicated:
-
-  - axis 1 = Y resolution = lines along X axis
-
-  - axis 2 = X resolution = lines along Y axis'
-from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: MetricsDataset
-attributes:
-  input:
-    name: input
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    alias: input
-    owner: ArgolightEDataset
-    domain_of:
-    - MetricsDataset
-    - FieldIlluminationDataset
-    - PSFBeadsDataset
-    - ArgolightBDataset
-    - ArgolightEDataset
-    range: ArgolightEInput
-  output:
-    name: output
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    alias: output
-    owner: ArgolightEDataset
-    domain_of:
-    - MetricsDataset
-    - FieldIlluminationDataset
-    - PSFBeadsDataset
-    - ArgolightBDataset
-    - ArgolightEDataset
-    range: ArgolightEOutput
-  microscope:
-    name: microscope
-    description: The microscope that was used to acquire the dataset
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: microscope
-    owner: ArgolightEDataset
-    domain_of:
-    - MetricsDataset
-    range: Microscope
-    required: true
-  sample:
-    name: sample
-    description: The sample that was imaged
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: sample
-    owner: ArgolightEDataset
-    domain_of:
-    - MetricsDataset
-    range: Sample
-  experimenter:
-    name: experimenter
-    description: The experimenter that performed the imaging experiment
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: experimenter
-    owner: ArgolightEDataset
-    domain_of:
-    - MetricsDataset
-    range: Experimenter
-  acquisition_datetime:
-    name: acquisition_datetime
-    description: The datetime of the acquisition
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: acquisition_datetime
-    owner: ArgolightEDataset
-    domain_of:
-    - MetricsDataset
-    - Image
-    range: datetime
-  processed:
-    name: processed
-    description: Has the dataset been processed by microscope-metrics
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    ifabsent: 'False'
-    alias: processed
-    owner: ArgolightEDataset
-    domain_of:
-    - MetricsDataset
-    range: boolean
-    required: true
-  data_reference:
-    name: data_reference
-    description: A reference to the data
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: data_reference
-    owner: ArgolightEDataset
-    domain_of:
-    - MetricsObject
-    range: DataReference
-    required: false
-  linked_references:
-    name: linked_references
-    description: A list of linked references
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: linked_references
-    owner: ArgolightEDataset
-    domain_of:
-    - MetricsObject
-    range: DataReference
-    required: false
-    inlined: true
-    inlined_as_list: true
-  name:
-    name: name
-    description: The human readable name of an entity
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: false
-    alias: name
-    owner: ArgolightEDataset
-    domain_of:
-    - NamedObject
-    - Experimenter
-    range: string
-    required: false
-  description:
-    name: description
-    description: A human readable description of an entity
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: false
-    alias: description
-    owner: ArgolightEDataset
-    domain_of:
-    - NamedObject
-    - Tag
-    range: string
-    required: false
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Class: ArgolightEKeyValues

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URI: microscopemetrics_schema:ArgolightEKeyValues

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classDiagram - class ArgolightEKeyValues - KeyValues <|-- ArgolightEKeyValues - - ArgolightEKeyValues : channel_nr - - ArgolightEKeyValues : data_reference - - ArgolightEKeyValues --> DataReference : data_reference - - ArgolightEKeyValues : description - - ArgolightEKeyValues : focus_slice - - ArgolightEKeyValues : linked_references - - ArgolightEKeyValues --> DataReference : linked_references - - ArgolightEKeyValues : name - - ArgolightEKeyValues : peak_height_A - - ArgolightEKeyValues : peak_height_B - - ArgolightEKeyValues : peak_position_A - - ArgolightEKeyValues : peak_position_B - - ArgolightEKeyValues : peak_prominence_A - - ArgolightEKeyValues : peak_prominence_B - - ArgolightEKeyValues : rayleigh_resolution_microns - - ArgolightEKeyValues : rayleigh_resolution_pixels - - -
-

Inheritance

- -

Slots

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
NameCardinality and RangeDescriptionInheritance
channel_nr0..*
Integer		The channel number to which the measurements applydirect
focus_slice0..*
Integer		Z position at which focus has been measureddirect
rayleigh_resolution_pixels0..*
Float		Rayleigh resolution measured in pixelsdirect
rayleigh_resolution_microns0..*
Float		Rayleigh resolution measured in micronsdirect
peak_position_A0..*
Float		Position, in pixels, of first peak in the intensity profilesdirect
peak_position_B0..*
Float		Position, in pixels, of second peak in the intensity profilesdirect
peak_height_A0..*
Float		Height of first peak in the intensity profilesdirect
peak_height_B0..*
Float		Height of second peak in the intensity profilesdirect
peak_prominence_A0..*
Float		Prominence of first peak in the intensity profilesdirect
peak_prominence_B0..*
Float		Prominence of second peak in the intensity profilesdirect
data_reference0..1
DataReference		A reference to the dataMetricsObject
linked_references0..*
DataReference		A list of linked referencesMetricsObject
name0..1
String		The human readable name of an entityNamedObject
description0..1
String		A human readable description of an entityNamedObject
-

Usages

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used byused intypeused
ArgolightEOutputkey_measurementsrangeArgolightEKeyValues
-

Identifier and Mapping Information

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Schema Source

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Mappings

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Mapping TypeMapped Value
selfmicroscopemetrics_schema:ArgolightEKeyValues
nativemicroscopemetrics_schema:ArgolightEKeyValues
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LinkML Source

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Direct

-
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name: ArgolightEKeyValues
-from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: KeyValues
-slots:
-- channel_nr
-- focus_slice
-- rayleigh_resolution_pixels
-- rayleigh_resolution_microns
-- peak_position_A
-- peak_position_B
-- peak_height_A
-- peak_height_B
-- peak_prominence_A
-- peak_prominence_B
-
-
-
-

Induced

-
-
name: ArgolightEKeyValues
-from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: KeyValues
-attributes:
-  channel_nr:
-    name: channel_nr
-    description: The channel number to which the measurements apply
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: channel_nr
-    owner: ArgolightEKeyValues
-    domain_of:
-    - PSFBeadsKeyValues
-    - ArgolightBIntensityKeyValues
-    - ArgolightEKeyValues
-    range: integer
-    minimum_value: 0
-  focus_slice:
-    name: focus_slice
-    description: Z position at which focus has been measured. One value per channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: focus_slice
-    owner: ArgolightEKeyValues
-    domain_of:
-    - ArgolightEKeyValues
-    range: integer
-    minimum_value: 0
-  rayleigh_resolution_pixels:
-    name: rayleigh_resolution_pixels
-    description: Rayleigh resolution measured in pixels. One value per channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: rayleigh_resolution_pixels
-    owner: ArgolightEKeyValues
-    domain_of:
-    - ArgolightEKeyValues
-    range: float
-  rayleigh_resolution_microns:
-    name: rayleigh_resolution_microns
-    description: Rayleigh resolution measured in microns. One value per channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: rayleigh_resolution_microns
-    owner: ArgolightEKeyValues
-    domain_of:
-    - ArgolightEKeyValues
-    range: float
-  peak_position_A:
-    name: peak_position_A
-    description: Position, in pixels, of first peak in the intensity profiles. One
-      value per channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: peak_position_A
-    owner: ArgolightEKeyValues
-    domain_of:
-    - ArgolightEKeyValues
-    range: float
-  peak_position_B:
-    name: peak_position_B
-    description: Position, in pixels, of second peak in the intensity profiles. One
-      value per channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: peak_position_B
-    owner: ArgolightEKeyValues
-    domain_of:
-    - ArgolightEKeyValues
-    range: float
-  peak_height_A:
-    name: peak_height_A
-    description: Height of first peak in the intensity profiles. One value per channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: peak_height_A
-    owner: ArgolightEKeyValues
-    domain_of:
-    - ArgolightEKeyValues
-    range: float
-  peak_height_B:
-    name: peak_height_B
-    description: Height of second peak in the intensity profiles. One value per channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: peak_height_B
-    owner: ArgolightEKeyValues
-    domain_of:
-    - ArgolightEKeyValues
-    range: float
-  peak_prominence_A:
-    name: peak_prominence_A
-    description: Prominence of first peak in the intensity profiles. One value per
-      channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: peak_prominence_A
-    owner: ArgolightEKeyValues
-    domain_of:
-    - ArgolightEKeyValues
-    range: float
-  peak_prominence_B:
-    name: peak_prominence_B
-    description: Prominence of second peak in the intensity profiles. One value per
-      channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: true
-    alias: peak_prominence_B
-    owner: ArgolightEKeyValues
-    domain_of:
-    - ArgolightEKeyValues
-    range: float
-  data_reference:
-    name: data_reference
-    description: A reference to the data
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: data_reference
-    owner: ArgolightEKeyValues
-    domain_of:
-    - MetricsObject
-    range: DataReference
-    required: false
-  linked_references:
-    name: linked_references
-    description: A list of linked references
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: linked_references
-    owner: ArgolightEKeyValues
-    domain_of:
-    - MetricsObject
-    range: DataReference
-    required: false
-    inlined: true
-    inlined_as_list: true
-  name:
-    name: name
-    description: The human readable name of an entity
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: false
-    alias: name
-    owner: ArgolightEKeyValues
-    domain_of:
-    - NamedObject
-    - Experimenter
-    range: string
-    required: false
-  description:
-    name: description
-    description: A human readable description of an entity
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-    rank: 1000
-    multivalued: false
-    alias: description
-    owner: ArgolightEKeyValues
-    domain_of:
-    - NamedObject
-    - Tag
-    range: string
-    required: false
-
-
-
-
-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/ArgolightEOutput/index.html b/ArgolightEOutput/index.html deleted file mode 100644 index 0f78f643..00000000 --- a/ArgolightEOutput/index.html +++ /dev/null @@ -1,578 +0,0 @@ - - - - - - - - - - -Class: ArgolightEOutput - microscopemetrics-schema - - - - - - - - - - - -
- - Skip to content - -
-
-
-
- -
-
-
-
-
-
-
- -
-
-
-
-
-
- -
-
-
-
-
- - - -

Class: ArgolightEOutput

-

URI: microscopemetrics_schema:ArgolightEOutput

-
classDiagram - class ArgolightEOutput - MetricsOutput <|-- ArgolightEOutput - - ArgolightEOutput : comment - - ArgolightEOutput --> Comment : comment - - ArgolightEOutput : errors - - ArgolightEOutput : intensity_profiles - - ArgolightEOutput --> Table : intensity_profiles - - ArgolightEOutput : key_measurements - - ArgolightEOutput --> ArgolightEKeyValues : key_measurements - - ArgolightEOutput : peaks_rois - - ArgolightEOutput --> Roi : peaks_rois - - ArgolightEOutput : processing_application - - ArgolightEOutput : processing_datetime - - ArgolightEOutput : processing_entity - - ArgolightEOutput : processing_log - - ArgolightEOutput : processing_version - - ArgolightEOutput : warnings - - -
-

Inheritance

- -

Slots

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
NameCardinality and RangeDescriptionInheritance
peaks_rois0..*
Roi		ROIs of the peaks found in the argolight imagesdirect
key_measurements0..1
ArgolightEKeyValues		Key Measurements on Argolight E imagesdirect
intensity_profiles0..1
Table		Intensity profiles of the argolight lines provided as tablesdirect
processing_application1..*
String		The application used to process the datasetMetricsOutput
processing_version1..*
String		The version of the application used to process the datasetMetricsOutput
processing_entity0..*
String		The entity that processed the datasetMetricsOutput
processing_datetime1..1
datetime		The datetime of the processing by microscope-metricsMetricsOutput
processing_log0..1
String		The log of the processing by microscope-metricsMetricsOutput
warnings0..*
String		The warnings of the processing by microscope-metricsMetricsOutput
errors0..*
String		The errors of the processing by microscope-metricsMetricsOutput
comment0..1
Comment		A human readable comment about the datasetMetricsOutput
-

Usages

- - - - - - - - - - - - - - - - - -
used byused intypeused
ArgolightEDatasetoutputrangeArgolightEOutput
-

Identifier and Mapping Information

-

Schema Source

-
    -
  • from schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
    • -
-

Mappings

- - - - - - - - - - - - - - - - - -
Mapping TypeMapped Value
selfmicroscopemetrics_schema:ArgolightEOutput
nativemicroscopemetrics_schema:ArgolightEOutput
-

LinkML Source

- -

Direct

-
-
name: ArgolightEOutput
-from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: MetricsOutput
-attributes:
-  peaks_rois:
-    name: peaks_rois
-    description: ROIs of the peaks found in the argolight images. One per channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    rank: 1000
-    multivalued: true
-    domain_of:
-    - ArgolightEOutput
-    range: Roi
-  key_measurements:
-    name: key_measurements
-    description: Key Measurements on Argolight E images
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    rank: 1000
-    multivalued: false
-    domain_of:
-    - ArgolightEOutput
-    range: ArgolightEKeyValues
-  intensity_profiles:
-    name: intensity_profiles
-    description: Intensity profiles of the argolight lines provided as tables. One
-      table per channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    multivalued: false
-    domain_of:
-    - FieldIlluminationOutput
-    - ArgolightEOutput
-    range: Table
-
-
-
-

Induced

-
-
name: ArgolightEOutput
-from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: MetricsOutput
-attributes:
-  peaks_rois:
-    name: peaks_rois
-    description: ROIs of the peaks found in the argolight images. One per channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    rank: 1000
-    multivalued: true
-    alias: peaks_rois
-    owner: ArgolightEOutput
-    domain_of:
-    - ArgolightEOutput
-    range: Roi
-  key_measurements:
-    name: key_measurements
-    description: Key Measurements on Argolight E images
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    rank: 1000
-    multivalued: false
-    alias: key_measurements
-    owner: ArgolightEOutput
-    domain_of:
-    - ArgolightEOutput
-    range: ArgolightEKeyValues
-  intensity_profiles:
-    name: intensity_profiles
-    description: Intensity profiles of the argolight lines provided as tables. One
-      table per channel
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/argolight_schema
-    multivalued: false
-    alias: intensity_profiles
-    owner: ArgolightEOutput
-    domain_of:
-    - FieldIlluminationOutput
-    - ArgolightEOutput
-    range: Table
-  processing_application:
-    name: processing_application
-    description: The application used to process the dataset
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: processing_application
-    owner: ArgolightEOutput
-    domain_of:
-    - MetricsOutput
-    range: string
-    required: true
-  processing_version:
-    name: processing_version
-    description: The version of the application used to process the dataset
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: processing_version
-    owner: ArgolightEOutput
-    domain_of:
-    - MetricsOutput
-    range: string
-    required: true
-  processing_entity:
-    name: processing_entity
-    description: The entity that processed the dataset
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: processing_entity
-    owner: ArgolightEOutput
-    domain_of:
-    - MetricsOutput
-    range: string
-    required: false
-  processing_datetime:
-    name: processing_datetime
-    description: The datetime of the processing by microscope-metrics
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: processing_datetime
-    owner: ArgolightEOutput
-    domain_of:
-    - MetricsOutput
-    range: datetime
-    required: true
-  processing_log:
-    name: processing_log
-    description: The log of the processing by microscope-metrics
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: processing_log
-    owner: ArgolightEOutput
-    domain_of:
-    - MetricsOutput
-    range: string
-    required: false
-  warnings:
-    name: warnings
-    description: The warnings of the processing by microscope-metrics
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: warnings
-    owner: ArgolightEOutput
-    domain_of:
-    - MetricsOutput
-    range: string
-    required: false
-  errors:
-    name: errors
-    description: The errors of the processing by microscope-metrics
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: errors
-    owner: ArgolightEOutput
-    domain_of:
-    - MetricsOutput
-    range: string
-    required: false
-  comment:
-    name: comment
-    description: A human readable comment about the dataset
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: false
-    alias: comment
-    owner: ArgolightEOutput
-    domain_of:
-    - MetricsOutput
-    range: Comment
-    required: false
-
-
-
-
-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/Boolean/index.html b/Boolean/index.html index 0bfefb65..fc5fc588 100644 --- a/Boolean/index.html +++ b/Boolean/index.html @@ -11,7 +11,7 @@ - + diff --git a/CentersFitted/index.html b/CentersFitted/index.html index 7ef3f01b..96f481bd 100644 --- a/CentersFitted/index.html +++ b/CentersFitted/index.html @@ -7,7 +7,7 @@ - + Class: CentersFitted - microscopemetrics-schema @@ -204,6 +204,7 @@

Class: CentersFitted

URI: microscopemetrics_schema:CentersFitted

classDiagram class CentersFitted + click CentersFitted href "../CentersFitted"
@@ -310,5 +311,7 @@

Induced

- + \ No newline at end of file diff --git a/CentersGeometric/index.html b/CentersGeometric/index.html index 09bb4f3f..49eec01a 100644 --- a/CentersGeometric/index.html +++ b/CentersGeometric/index.html @@ -7,7 +7,7 @@ - + Class: CentersGeometric - microscopemetrics-schema @@ -204,6 +204,7 @@

Class: CentersGeometric

URI: microscopemetrics_schema:CentersGeometric

classDiagram class CentersGeometric + click CentersGeometric href "../CentersGeometric"
@@ -310,5 +311,7 @@

Induced

- + \ No newline at end of file diff --git a/CentersMaxIntensity/index.html b/CentersMaxIntensity/index.html index e3301702..500c95ae 100644 --- a/CentersMaxIntensity/index.html +++ b/CentersMaxIntensity/index.html @@ -7,7 +7,7 @@ - + Class: CentersMaxIntensity - microscopemetrics-schema @@ -204,6 +204,7 @@

Class: CentersMaxIntensity

URI: microscopemetrics_schema:CentersMaxIntensity

classDiagram class CentersMaxIntensity + click CentersMaxIntensity href "../CentersMaxIntensity"
@@ -312,5 +313,7 @@

Induced

- + \ No newline at end of file diff --git a/CentersOfMass/index.html b/CentersOfMass/index.html index 9adeee72..3d8fc426 100644 --- a/CentersOfMass/index.html +++ b/CentersOfMass/index.html @@ -7,7 +7,7 @@ - + Class: CentersOfMass - microscopemetrics-schema @@ -204,8 +204,7 @@

Class: CentersOfMass

URI: microscopemetrics_schema:CentersOfMass

classDiagram class CentersOfMass - CentersOfMass <|-- ArgolightBCentersOfMass - + click CentersOfMass href "../CentersOfMass"
@@ -238,7 +237,7 @@

Mixin Usage

-ArgolightBCentersOfMass + @@ -312,5 +311,7 @@

Induced

- + \ No newline at end of file diff --git a/Channel/index.html b/Channel/index.html index f4bd3693..15de9af7 100644 --- a/Channel/index.html +++ b/Channel/index.html @@ -7,7 +7,7 @@ - + Class: Channel - microscopemetrics-schema @@ -209,7 +209,18 @@

Class: Channel

URI: microscopemetrics_schema:Channel

classDiagram class Channel - NamedObject <|-- Channel + click Channel href "../Channel" + MetricsObject <|-- Channel + click MetricsObject href "../MetricsObject" + + Channel : data_reference + + + + + Channel --> "0..1" DataReference : data_reference + click DataReference href "../DataReference" + Channel : description @@ -217,6 +228,15 @@

Class: Channel

Channel : excitation_wavelength_nm + Channel : linked_references + + + + + Channel --> "*" DataReference : linked_references + click DataReference href "../DataReference" + + Channel : name @@ -224,10 +244,13 @@

Class: Channel

Inheritance

Slots

@@ -252,6 +275,18 @@

Slots

+ + + + + + + + + + + + @@ -315,7 +350,7 @@

Direct

name: Channel
 description: A image channel
 from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: NamedObject
+is_a: MetricsObject
 slots:
 - excitation_wavelength_nm
 - emission_wavelength_nm
@@ -327,38 +362,63 @@ 
Induced

 
name: Channel
 description: A image channel
 from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: NamedObject
+is_a: MetricsObject
 attributes:
   excitation_wavelength_nm:
     name: excitation_wavelength_nm
     description: The excitation wavelength in nm
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: false
     alias: excitation_wavelength_nm
     owner: Channel
     domain_of:
     - Channel
     range: float
     required: false
+    multivalued: false
   emission_wavelength_nm:
     name: emission_wavelength_nm
     description: The emission wavelength in nm
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: false
     alias: emission_wavelength_nm
     owner: Channel
     domain_of:
     - Channel
     range: float
     required: false
+    multivalued: false
+  data_reference:
+    name: data_reference
+    description: A reference to the data
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
+    rank: 1000
+    alias: data_reference
+    owner: Channel
+    domain_of:
+    - MetricsObject
+    range: DataReference
+    required: false
+    multivalued: false
+  linked_references:
+    name: linked_references
+    description: A list of linked references
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
+    rank: 1000
+    alias: linked_references
+    owner: Channel
+    domain_of:
+    - MetricsObject
+    range: DataReference
+    required: false
+    multivalued: true
+    inlined: true
+    inlined_as_list: true
   name:
     name: name
     description: The human readable name of an entity
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: false
     alias: name
     owner: Channel
     domain_of:
@@ -366,12 +426,12 @@ 
Induced

     - Experimenter
     range: string
     required: false
+    multivalued: false
   description:
     name: description
     description: A human readable description of an entity
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: false
     alias: description
     owner: Channel
     domain_of:
@@ -379,6 +439,7 @@ 
Induced

     - Tag
     range: string
     required: false
+    multivalued: false
 
 

 
@@ -407,5 +468,7 @@ 
Induced

 
 
 
-
+
 
\ No newline at end of file
diff --git a/ChannelSeries/index.html b/ChannelSeries/index.html
index d25abf59..a93eb16e 100644
--- a/ChannelSeries/index.html
+++ b/ChannelSeries/index.html
@@ -7,7 +7,7 @@
 
 
 
-
+
 Class: ChannelSeries - microscopemetrics-schema
 
 
@@ -204,9 +204,15 @@ 
Class: ChannelSeries

 
URI: microscopemetrics_schema:ChannelSeries

 
 classDiagram
     class ChannelSeries
+    click ChannelSeries href "../ChannelSeries"
       ChannelSeries : channels
 
-          ChannelSeries --> Channel : channels
+
+
+
+    ChannelSeries --> "1..*" Channel : channels
+    click Channel href "../Channel"
+
 
 
 

@@ -225,7 +231,7 @@ 
Slots
- + @@ -293,13 +299,14 @@

Direct

name: channels implements: - linkml:elements + description: The channels of the ChannelSeries from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true domain_of: - ChannelSeries range: Channel required: true + multivalued: true @@ -315,15 +322,16 @@

Induced

name: channels implements: - linkml:elements + description: The channels of the ChannelSeries from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: channels owner: ChannelSeries domain_of: - ChannelSeries range: Channel required: true + multivalued: true @@ -352,5 +360,7 @@

Induced

- + \ No newline at end of file diff --git a/Color/index.html b/Color/index.html index 5b7f329b..30fc1079 100644 --- a/Color/index.html +++ b/Color/index.html @@ -7,7 +7,7 @@ - +Class: Color - microscopemetrics-schema @@ -204,6 +204,7 @@

Class: Color

URI: microscopemetrics_schema:Color

classDiagram class Color + click Color href "../Color" Color : alpha Color : b @@ -228,19 +229,19 @@

Slots

- + - + - + @@ -386,12 +387,12 @@

Direct

description: The red value of the color from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: int(128) domain_of: - Color range: integer required: true + multivalued: false minimum_value: 0 maximum_value: 255 g: @@ -399,12 +400,12 @@

Direct

description: The green value of the color from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: int(128) domain_of: - Color range: integer required: true + multivalued: false minimum_value: 0 maximum_value: 255 b: @@ -412,12 +413,12 @@

Direct

description: The blue value of the color from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: int(128) domain_of: - Color range: integer required: true + multivalued: false minimum_value: 0 maximum_value: 255 alpha: @@ -425,12 +426,12 @@

Direct

description: The alpha value of the color (optional) from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: int(255) domain_of: - Color range: integer required: false + multivalued: false minimum_value: 0 maximum_value: 255 @@ -447,7 +448,6 @@

Induced

description: The red value of the color from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: int(128) alias: r owner: Color @@ -455,6 +455,7 @@

Induced

- Color range: integer required: true + multivalued: false minimum_value: 0 maximum_value: 255 g: @@ -462,7 +463,6 @@

Induced

description: The green value of the color from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: int(128) alias: g owner: Color @@ -470,6 +470,7 @@

Induced

- Color range: integer required: true + multivalued: false minimum_value: 0 maximum_value: 255 b: @@ -477,7 +478,6 @@

Induced

description: The blue value of the color from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: int(128) alias: b owner: Color @@ -485,6 +485,7 @@

Induced

- Color range: integer required: true + multivalued: false minimum_value: 0 maximum_value: 255 alpha: @@ -492,7 +493,6 @@

Induced

description: The alpha value of the color (optional) from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: int(255) alias: alpha owner: Color @@ -500,6 +500,7 @@

Induced

- Color range: integer required: false + multivalued: false minimum_value: 0 maximum_value: 255 @@ -530,5 +531,7 @@

Induced

- + \ No newline at end of file diff --git a/Column/index.html b/Column/index.html index 058d3b35..b14e0df2 100644 --- a/Column/index.html +++ b/Column/index.html @@ -7,7 +7,7 @@ - +Class: Column - microscopemetrics-schema @@ -209,7 +209,11 @@

Class: Column

URI: microscopemetrics_schema:Column

classDiagram class Column + click Column href "../Column" NamedObject <|-- Column + click NamedObject href "../NamedObject" + + Column : data_type Column : description @@ -217,7 +221,14 @@

Class: Column

Column : source_reference - Column --> DataReference : source_reference + + + + Column --> "0..1" DataReference : source_reference + click DataReference href "../DataReference" + + + Column : values
@@ -246,6 +257,18 @@

Slots

+ + + + + + + + + + + + @@ -271,7 +294,7 @@

Usages

- + @@ -316,11 +339,32 @@

Direct

description: The source object of the column from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - Column range: DataReference required: false + multivalued: false + data_type: + name: data_type + description: The data type of the column + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema + rank: 1000 + ifabsent: string(str) + domain_of: + - Column + range: string + required: true + multivalued: false + values: + name: values + description: An optional container for the values of the column + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema + domain_of: + - TimeSeries + - Column + range: string + required: false + multivalued: true @@ -336,19 +380,43 @@

Induced

description: The source object of the column from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: source_reference owner: Column domain_of: - Column range: DataReference required: false + multivalued: false + data_type: + name: data_type + description: The data type of the column + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema + rank: 1000 + ifabsent: string(str) + alias: data_type + owner: Column + domain_of: + - Column + range: string + required: true + multivalued: false + values: + name: values + description: An optional container for the values of the column + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema + alias: values + owner: Column + domain_of: + - TimeSeries + - Column + range: string + required: false + multivalued: true name: name: name description: The human readable name of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: name owner: Column domain_of: @@ -356,12 +424,12 @@

Induced

- Experimenter range: string required: false + multivalued: false description: name: description description: A human readable description of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: description owner: Column domain_of: @@ -369,6 +437,7 @@

Induced

- Tag range: string required: false + multivalued: false @@ -397,5 +466,7 @@

Induced

- + \ No newline at end of file diff --git a/Comment/index.html b/Comment/index.html index c1542fb0..e94f1a43 100644 --- a/Comment/index.html +++ b/Comment/index.html @@ -7,7 +7,7 @@ - +Class: Comment - microscopemetrics-schema @@ -204,13 +204,24 @@

Class: Comment

URI: microscopemetrics_schema:Comment

classDiagram class Comment + click Comment href "../Comment" Comment : author - Comment --> Experimenter : author + + + + Comment --> "0..1" Experimenter : author + click Experimenter href "../Experimenter" + Comment : comment_type - Comment --> CommentTypesEnum : comment_type + + + + Comment --> "1" CommentTypesEnum : comment_type + click CommentTypesEnum href "../CommentTypesEnum" + Comment : datetime @@ -232,7 +243,7 @@

Slots

- + @@ -244,13 +255,13 @@

Slots

- + - + @@ -291,18 +302,6 @@

Usages

- - - - - - - - - - - -
direct
data_reference0..1
DataReference		A reference to the dataMetricsObject
linked_references*
DataReference		A list of linked referencesMetricsObject
name 0..1
String		 The human readable name of an entity
channels 1..*
Channel		The channels of the ChannelSeries direct
r1..1
Integer		1
Integer		 The red value of the color direct
g1..1
Integer		1
Integer		 The green value of the color direct
b1..1
Integer		1
Integer		 The blue value of the color direct
direct
data_type1
String		The data type of the columndirect
values*
String		An optional container for the values of the columndirect
name 0..1
String		 The human readable name of an entity
ColumnSeriesTable columns range Column
datetime1..1
datetime		1
datetime		 The datetime to which the comment is referring direct
comment_type1..1
CommentTypesEnum		1
CommentTypesEnum		 The type of the comment direct
text1..1
String		1
String		 The text of the comment direct
range Comment
ArgolightBOutputcommentrangeComment
ArgolightEOutputcommentrangeComment

Identifier and Mapping Information

@@ -342,41 +341,41 @@

Direct

description: The datetime to which the comment is referring from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - Comment range: datetime required: true + multivalued: false author: name: author description: The author of the comment from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - Comment range: Experimenter required: false + multivalued: false comment_type: name: comment_type description: The type of the comment from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - Comment range: CommentTypesEnum required: true + multivalued: false text: name: text description: The text of the comment from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - Comment range: string required: true + multivalued: false @@ -391,49 +390,49 @@

Induced

description: The datetime to which the comment is referring from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: datetime owner: Comment domain_of: - Comment range: datetime required: true + multivalued: false author: name: author description: The author of the comment from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: author owner: Comment domain_of: - Comment range: Experimenter required: false + multivalued: false comment_type: name: comment_type description: The type of the comment from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: comment_type owner: Comment domain_of: - Comment range: CommentTypesEnum required: true + multivalued: false text: name: text description: The text of the comment from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: text owner: Comment domain_of: - Comment range: string required: true + multivalued: false @@ -462,5 +461,7 @@

Induced

- + \ No newline at end of file diff --git a/CommentTypesEnum/index.html b/CommentTypesEnum/index.html index 82534493..caf0b7c1 100644 --- a/CommentTypesEnum/index.html +++ b/CommentTypesEnum/index.html @@ -11,7 +11,7 @@ - + diff --git a/key_values/index.html b/CriticalParameter/index.html similarity index 88% rename from key_values/index.html rename to CriticalParameter/index.html index 8dab124d..a206d1a3 100644 --- a/key_values/index.html +++ b/CriticalParameter/index.html @@ -8,14 +8,14 @@ - + - + - Slot: key_values - microscopemetrics-schema + Subset: CriticalParameter - microscopemetrics-schema @@ -64,7 +64,7 @@
- + Skip to content @@ -97,7 +97,7 @@
- Slot: key_values + Subset: CriticalParameter
@@ -255,32 +255,24 @@ @@ -297,56 +289,20 @@ - + -

Slot: key_values

-

URI: microscopemetrics_schema:key_values

- - -

Applicable Classes

- - - - - - - - - - - - - - - - - - - - -
NameDescriptionModifies Slot
FieldIlluminationOutputno
PSFBeadsOutputno
-

Properties

+

Subset: CriticalParameter

+

A subset indicating that changing this parameter may damage the consistency of the analysis.

+

URI: CriticalParameter

+

Identifier and Mapping Information

+

Schema Source

-

Identifier and Mapping Information

-

LinkML Source

-
- -
name: key_values
-alias: key_values
-domain_of:
-- FieldIlluminationOutput
-- PSFBeadsOutput
-range: string
-
-
- -
diff --git a/Curie/index.html b/Curie/index.html index 714f1963..331cfaf0 100644 --- a/Curie/index.html +++ b/Curie/index.html @@ -11,7 +11,7 @@ - + diff --git a/DataReference/index.html b/DataReference/index.html index 2bd203f9..ed110255 100644 --- a/DataReference/index.html +++ b/DataReference/index.html @@ -7,7 +7,7 @@ - + Class: DataReference - microscopemetrics-schema @@ -204,6 +204,7 @@

Class: DataReference

URI: microscopemetrics_schema:DataReference

classDiagram class DataReference + click DataReference href "../DataReference" DataReference : data_uri DataReference : omero_host @@ -212,7 +213,12 @@

Class: DataReference

DataReference : omero_object_type - DataReference --> OMEROObjectTypeEnum : omero_object_type + + + + DataReference --> "0..1" OMEROObjectTypeEnum : omero_object_type + click OMEROObjectTypeEnum href "../OMEROObjectTypeEnum" + DataReference : omero_port @@ -370,175 +376,127 @@

Usages

DataReference -Column -source_reference -range -DataReference - - -Roi -data_reference -range -DataReference - - -Roi -linked_references -range -DataReference - - -KeyValues -data_reference -range -DataReference - - -KeyValues -linked_references -range -DataReference - - -Tag -data_reference -range -DataReference - - -Tag -linked_references -range -DataReference - - -Table +Channel data_reference range DataReference -Table +Channel linked_references range DataReference -FieldIlluminationDataset -data_reference -range -DataReference - - -FieldIlluminationDataset -linked_references +Column +source_reference range DataReference -FieldIlluminationKeyValues +Roi data_reference range DataReference -FieldIlluminationKeyValues +Roi linked_references range DataReference -PSFBeadsDataset +KeyValues data_reference range DataReference -PSFBeadsDataset +KeyValues linked_references range DataReference -PSFBeadsKeyValues +KeyMeasurements data_reference range DataReference -PSFBeadsKeyValues +KeyMeasurements linked_references range DataReference -ArgolightBDataset +Tag data_reference range DataReference -ArgolightBDataset +Tag linked_references range DataReference -ArgolightBCentersOfMass +Table data_reference range DataReference -ArgolightBCentersOfMass +Table linked_references range DataReference -ArgolightBIntensityKeyValues +FieldIlluminationDataset data_reference range DataReference -ArgolightBIntensityKeyValues +FieldIlluminationDataset linked_references range DataReference -ArgolightBDistanceKeyValues +FieldIlluminationKeyMeasurements data_reference range DataReference -ArgolightBDistanceKeyValues +FieldIlluminationKeyMeasurements linked_references range DataReference -ArgolightEDataset +PSFBeadsDataset data_reference range DataReference -ArgolightEDataset +PSFBeadsDataset linked_references range DataReference -ArgolightEKeyValues +PSFBeadsKeyMeasurements data_reference range DataReference -ArgolightEKeyValues +PSFBeadsKeyMeasurements linked_references range DataReference @@ -722,5 +680,7 @@

Induced

- + \ No newline at end of file diff --git a/Date/index.html b/Date/index.html index cb0dbb03..ed61b5a5 100644 --- a/Date/index.html +++ b/Date/index.html @@ -11,7 +11,7 @@ - + diff --git a/DateOrDatetime/index.html b/DateOrDatetime/index.html index 96092dae..7fa969f9 100644 --- a/DateOrDatetime/index.html +++ b/DateOrDatetime/index.html @@ -11,7 +11,7 @@ - + diff --git a/Datetime/index.html b/Datetime/index.html index 43822e48..2cbafeac 100644 --- a/Datetime/index.html +++ b/Datetime/index.html @@ -11,7 +11,7 @@ - + diff --git a/Decimal/index.html b/Decimal/index.html index 21b2bc0e..06fd88d7 100644 --- a/Decimal/index.html +++ b/Decimal/index.html @@ -11,7 +11,7 @@ - + diff --git a/Double/index.html b/Double/index.html index 92dcaa2b..5ec52cec 100644 --- a/Double/index.html +++ b/Double/index.html @@ -11,7 +11,7 @@ - + diff --git a/Ellipse/index.html b/Ellipse/index.html index 67f523d2..828eebd6 100644 --- a/Ellipse/index.html +++ b/Ellipse/index.html @@ -7,7 +7,7 @@ - + Class: Ellipse - microscopemetrics-schema @@ -209,7 +209,9 @@

Class: Ellipse

URI: microscopemetrics_schema:Ellipse

classDiagram class Ellipse + click Ellipse href "../Ellipse" Shape <|-- Ellipse + click Shape href "../Shape" Ellipse : c @@ -217,13 +219,23 @@

Class: Ellipse

Ellipse : fill_color - Ellipse --> Color : fill_color + + + + Ellipse --> "0..1" Color : fill_color + click Color href "../Color" + Ellipse : name Ellipse : stroke_color - Ellipse --> Color : stroke_color + + + + Ellipse --> "0..1" Color : stroke_color + click Color href "../Color" + Ellipse : stroke_width @@ -264,25 +276,25 @@

Slots

x -1..1
Float +1
Float The x coordinate of the bounding box of the ellipse direct y -1..1
Float +1
Float The y coordinate of the bounding box of the ellipse direct x_rad -1..1
Float +1
Float The x radius of the ellipse direct y_rad -1..1
Float +1
Float The y radius of the ellipse direct @@ -353,12 +365,6 @@

Usages

range Ellipse - -ArgolightBCentersOfMass -ellipses -range -Ellipse -

Identifier and Mapping Information

@@ -398,7 +404,6 @@

Direct

name: x description: The x coordinate of the bounding box of the ellipse from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - multivalued: false domain_of: - Point - Rectangle @@ -407,11 +412,11 @@

Direct

- Mask range: float required: true + multivalued: false y: name: y description: The y coordinate of the bounding box of the ellipse from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - multivalued: false domain_of: - Point - Rectangle @@ -420,26 +425,27 @@

Direct

- Mask range: float required: true + multivalued: false x_rad: name: x_rad description: The x radius of the ellipse from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - Ellipse range: float required: true + multivalued: false y_rad: name: y_rad description: The y radius of the ellipse from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - Ellipse range: float required: true + multivalued: false @@ -454,7 +460,6 @@

Induced

name: x description: The x coordinate of the bounding box of the ellipse from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - multivalued: false alias: x owner: Ellipse domain_of: @@ -465,11 +470,11 @@

Induced

- Mask range: float required: true + multivalued: false y: name: y description: The y coordinate of the bounding box of the ellipse from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - multivalued: false alias: y owner: Ellipse domain_of: @@ -480,30 +485,31 @@

Induced

- Mask range: float required: true + multivalued: false x_rad: name: x_rad description: The x radius of the ellipse from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: x_rad owner: Ellipse domain_of: - Ellipse range: float required: true + multivalued: false y_rad: name: y_rad description: The y radius of the ellipse from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: y_rad owner: Ellipse domain_of: - Ellipse range: float required: true + multivalued: false z: name: z description: The z coordinate of the shape @@ -576,7 +582,6 @@

Induced

description: The human readable name of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: name owner: Ellipse domain_of: @@ -584,12 +589,12 @@

Induced

- Experimenter range: string required: false + multivalued: false description: name: description description: A human readable description of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: description owner: Ellipse domain_of: @@ -597,6 +602,7 @@

Induced

- Tag range: string required: false + multivalued: false @@ -625,5 +631,7 @@

Induced

- + \ No newline at end of file diff --git a/Experimenter/index.html b/Experimenter/index.html index 418a822c..4dccbfce 100644 --- a/Experimenter/index.html +++ b/Experimenter/index.html @@ -7,7 +7,7 @@ - + Class: Experimenter - microscopemetrics-schema @@ -204,6 +204,7 @@

Class: Experimenter

URI: microscopemetrics_schema:Experimenter

classDiagram class Experimenter + click Experimenter href "../Experimenter" Experimenter : name Experimenter : orcid @@ -224,13 +225,13 @@

Slots

name -1..1
String +1
String The name of the experimenter direct orcid -1..1
String +1
String The ORCID of the experimenter direct @@ -277,18 +278,6 @@

Usages

range Experimenter - -ArgolightBDataset -experimenter -range -Experimenter - - -ArgolightEDataset -experimenter -range -Experimenter -

Identifier and Mapping Information

@@ -402,5 +391,7 @@

Induced

- + \ No newline at end of file diff --git a/FieldIlluminationDataset/index.html b/FieldIlluminationDataset/index.html index 5064702a..c242847b 100644 --- a/FieldIlluminationDataset/index.html +++ b/FieldIlluminationDataset/index.html @@ -7,7 +7,7 @@ - + Class: FieldIlluminationDataset - microscopemetrics-schema @@ -204,43 +204,89 @@

Class: FieldIlluminationDataset

URI: microscopemetrics_schema:FieldIlluminationDataset

classDiagram class FieldIlluminationDataset + click FieldIlluminationDataset href "../FieldIlluminationDataset" MetricsDataset <|-- FieldIlluminationDataset + click MetricsDataset href "../MetricsDataset" FieldIlluminationDataset : acquisition_datetime FieldIlluminationDataset : data_reference - FieldIlluminationDataset --> DataReference : data_reference + + + + FieldIlluminationDataset --> "0..1" DataReference : data_reference + click DataReference href "../DataReference" + FieldIlluminationDataset : description FieldIlluminationDataset : experimenter - FieldIlluminationDataset --> Experimenter : experimenter - FieldIlluminationDataset : input - FieldIlluminationDataset --> FieldIlluminationInput : input + + FieldIlluminationDataset --> "0..1" Experimenter : experimenter + click Experimenter href "../Experimenter" + + + FieldIlluminationDataset : input_data + + + + + FieldIlluminationDataset --> "0..1" FieldIlluminationInputData : input_data + click FieldIlluminationInputData href "../FieldIlluminationInputData" + + + FieldIlluminationDataset : input_parameters + + + + + FieldIlluminationDataset --> "0..1" FieldIlluminationInputParameters : input_parameters + click FieldIlluminationInputParameters href "../FieldIlluminationInputParameters" + FieldIlluminationDataset : linked_references - FieldIlluminationDataset --> DataReference : linked_references + + + + FieldIlluminationDataset --> "*" DataReference : linked_references + click DataReference href "../DataReference" + FieldIlluminationDataset : microscope - FieldIlluminationDataset --> Microscope : microscope + + + + FieldIlluminationDataset --> "1" Microscope : microscope + click Microscope href "../Microscope" + FieldIlluminationDataset : name FieldIlluminationDataset : output - FieldIlluminationDataset --> FieldIlluminationOutput : output + + + + FieldIlluminationDataset --> "0..1" FieldIlluminationOutput : output + click FieldIlluminationOutput href "../FieldIlluminationOutput" + FieldIlluminationDataset : processed FieldIlluminationDataset : sample - FieldIlluminationDataset --> Sample : sample + + + + FieldIlluminationDataset --> "0..1" HomogeneousField : sample + click HomogeneousField href "../HomogeneousField" +
@@ -269,8 +315,14 @@

Slots

-input -0..1
FieldIlluminationInput +input_data +0..1
FieldIlluminationInputData + +direct + + +input_parameters +0..1
FieldIlluminationInputParameters direct @@ -281,15 +333,15 @@

Slots

direct -microscope -1..1
Microscope -The microscope that was used to acquire the dataset -MetricsDataset +sample +0..1
HomogeneousField + +direct -sample -0..1
Sample -The sample that was imaged +microscope +1
Microscope +The microscope that was used to acquire the dataset MetricsDataset @@ -306,7 +358,7 @@

Slots

processed -1..1
Boolean +1
Boolean Has the dataset been processed by microscope-metrics MetricsDataset @@ -318,7 +370,7 @@

Slots

linked_references -0..*
DataReference +*
DataReference A list of linked references MetricsObject @@ -369,26 +421,38 @@

Direct

from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema is_a: MetricsDataset attributes: - input: - name: input - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + input_data: + name: input_data + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema + domain_of: + - MetricsDataset + - FieldIlluminationDataset + - PSFBeadsDataset + range: FieldIlluminationInputData + input_parameters: + name: input_parameters + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema domain_of: - MetricsDataset - FieldIlluminationDataset - PSFBeadsDataset - - ArgolightBDataset - - ArgolightEDataset - range: FieldIlluminationInput + range: FieldIlluminationInputParameters output: name: output - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema domain_of: - MetricsDataset - FieldIlluminationDataset - PSFBeadsDataset - - ArgolightBDataset - - ArgolightEDataset range: FieldIlluminationOutput + sample: + name: sample + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema + domain_of: + - MetricsDataset + - FieldIlluminationDataset + - PSFBeadsDataset + range: HomogeneousField @@ -399,82 +463,83 @@

Induced

from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema is_a: MetricsDataset attributes: - input: - name: input - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema - alias: input + input_data: + name: input_data + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema + alias: input_data + owner: FieldIlluminationDataset + domain_of: + - MetricsDataset + - FieldIlluminationDataset + - PSFBeadsDataset + range: FieldIlluminationInputData + input_parameters: + name: input_parameters + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema + alias: input_parameters owner: FieldIlluminationDataset domain_of: - MetricsDataset - FieldIlluminationDataset - PSFBeadsDataset - - ArgolightBDataset - - ArgolightEDataset - range: FieldIlluminationInput + range: FieldIlluminationInputParameters output: name: output - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema alias: output owner: FieldIlluminationDataset domain_of: - MetricsDataset - FieldIlluminationDataset - PSFBeadsDataset - - ArgolightBDataset - - ArgolightEDataset range: FieldIlluminationOutput + sample: + name: sample + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema + alias: sample + owner: FieldIlluminationDataset + domain_of: + - MetricsDataset + - FieldIlluminationDataset + - PSFBeadsDataset + range: HomogeneousField microscope: name: microscope description: The microscope that was used to acquire the dataset from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 - multivalued: false alias: microscope owner: FieldIlluminationDataset domain_of: - MetricsDataset range: Microscope required: true - sample: - name: sample - description: The sample that was imaged - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 multivalued: false - alias: sample - owner: FieldIlluminationDataset - domain_of: - - MetricsDataset - range: Sample experimenter: name: experimenter description: The experimenter that performed the imaging experiment from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 - multivalued: false alias: experimenter owner: FieldIlluminationDataset domain_of: - MetricsDataset range: Experimenter + multivalued: false acquisition_datetime: name: acquisition_datetime description: The datetime of the acquisition from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 - multivalued: false alias: acquisition_datetime owner: FieldIlluminationDataset domain_of: - MetricsDataset - Image range: datetime + multivalued: false processed: name: processed description: Has the dataset been processed by microscope-metrics from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: 'False' alias: processed owner: FieldIlluminationDataset @@ -482,30 +547,31 @@

Induced

- MetricsDataset range: boolean required: true + multivalued: false data_reference: name: data_reference description: A reference to the data from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: data_reference owner: FieldIlluminationDataset domain_of: - MetricsObject range: DataReference required: false + multivalued: false linked_references: name: linked_references description: A list of linked references from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: linked_references owner: FieldIlluminationDataset domain_of: - MetricsObject range: DataReference required: false + multivalued: true inlined: true inlined_as_list: true name: @@ -513,7 +579,6 @@

Induced

description: The human readable name of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: name owner: FieldIlluminationDataset domain_of: @@ -521,12 +586,12 @@

Induced

- Experimenter range: string required: false + multivalued: false description: name: description description: A human readable description of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: description owner: FieldIlluminationDataset domain_of: @@ -534,6 +599,7 @@

Induced

- Tag range: string required: false + multivalued: false @@ -562,5 +628,7 @@

Induced

- + \ No newline at end of file diff --git a/FieldIlluminationInputData/index.html b/FieldIlluminationInputData/index.html new file mode 100644 index 00000000..d4b250a7 --- /dev/null +++ b/FieldIlluminationInputData/index.html @@ -0,0 +1,360 @@ + + + + + + + + + + +Class: FieldIlluminationInputData - microscopemetrics-schema + + + + + + + + + + + +
+ + Skip to content + +
+
+
+
+ +
+
+
+
+
+
+
+ +
+
+
+
+
+
+ +
+
+
+
+
+ + + +

Class: FieldIlluminationInputData

+

URI: microscopemetrics_schema:FieldIlluminationInputData

+
classDiagram + class FieldIlluminationInputData + click FieldIlluminationInputData href "../FieldIlluminationInputData" + MetricsInputData <|-- FieldIlluminationInputData + click MetricsInputData href "../MetricsInputData" + + FieldIlluminationInputData : field_illumination_image + + + + + FieldIlluminationInputData --> "1..*" Image : field_illumination_image + click Image href "../Image" + + + +
+

Inheritance

+ +

Slots

+ + + + + + + + + + + + + + + + + +
NameCardinality and RangeDescriptionInheritance
field_illumination_image1..*
Image		Input parameter: homogeneity image provided in the order TZYXCdirect
+

Usages

+ + + + + + + + + + + + + + + + + +
used byused intypeused
FieldIlluminationDatasetinput_datarangeFieldIlluminationInputData
+

Identifier and Mapping Information

+

Schema Source

+
    +
  • from schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
    • +
+

Mappings

+ + + + + + + + + + + + + + + + + +
Mapping TypeMapped Value
selfmicroscopemetrics_schema:FieldIlluminationInputData
nativemicroscopemetrics_schema:FieldIlluminationInputData
+

LinkML Source

+ +

Direct

+
+
name: FieldIlluminationInputData
+from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+is_a: MetricsInputData
+slots:
+- field_illumination_image
+
+
+
+

Induced

+
+
name: FieldIlluminationInputData
+from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+is_a: MetricsInputData
+attributes:
+  field_illumination_image:
+    name: field_illumination_image
+    description: 'Input parameter: homogeneity image provided in the order TZYXC.
+      While the analysis accepts multiple channels, the T and Z dimensions are expected
+      to be 1.'
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+    rank: 1000
+    alias: field_illumination_image
+    owner: FieldIlluminationInputData
+    domain_of:
+    - FieldIlluminationInputData
+    range: Image
+    required: true
+    multivalued: true
+    inlined: true
+    inlined_as_list: true
+
+
+
+
+
+ +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/FieldIlluminationInput/index.html b/FieldIlluminationInputParameters/index.html similarity index 83% rename from FieldIlluminationInput/index.html rename to FieldIlluminationInputParameters/index.html index 697d4acc..e8e0ed78 100644 --- a/FieldIlluminationInput/index.html +++ b/FieldIlluminationInputParameters/index.html @@ -5,10 +5,10 @@ - + - -Class: FieldIlluminationInput - microscopemetrics-schema + +Class: FieldIlluminationInputParameters - microscopemetrics-schema @@ -21,7 +21,7 @@
- + Skip to content
@@ -45,7 +45,7 @@
- Class: FieldIlluminationInput + Class: FieldIlluminationInputParameters
@@ -201,33 +201,31 @@
- + -

Class: FieldIlluminationInput

-

URI: microscopemetrics_schema:FieldIlluminationInput

+

Class: FieldIlluminationInputParameters

+

URI: microscopemetrics_schema:FieldIlluminationInputParameters

classDiagram - class FieldIlluminationInput - MetricsInput <|-- FieldIlluminationInput + class FieldIlluminationInputParameters + click FieldIlluminationInputParameters href "../FieldIlluminationInputParameters" + MetricsInputParameters <|-- FieldIlluminationInputParameters + click MetricsInputParameters href "../MetricsInputParameters" - FieldIlluminationInput : bit_depth + FieldIlluminationInputParameters : bit_depth - FieldIlluminationInput : corner_fraction + FieldIlluminationInputParameters : corner_fraction - FieldIlluminationInput : field_illumination_image + FieldIlluminationInputParameters : saturation_threshold - FieldIlluminationInput --> Image : field_illumination_image - - FieldIlluminationInput : saturation_threshold - - FieldIlluminationInput : sigma + FieldIlluminationInputParameters : sigma

Inheritance

- + \ No newline at end of file diff --git a/FieldIlluminationKeyValues/index.html b/FieldIlluminationKeyMeasurements/index.html similarity index 74% rename from FieldIlluminationKeyValues/index.html rename to FieldIlluminationKeyMeasurements/index.html index 4e1d2231..d5df711e 100644 --- a/FieldIlluminationKeyValues/index.html +++ b/FieldIlluminationKeyMeasurements/index.html @@ -5,10 +5,10 @@ - + - -Class: FieldIlluminationKeyValues - microscopemetrics-schema + +Class: FieldIlluminationKeyMeasurements - microscopemetrics-schema @@ -21,7 +21,7 @@
- + Skip to content
@@ -45,7 +45,7 @@
- Class: FieldIlluminationKeyValues + Class: FieldIlluminationKeyMeasurements
@@ -201,110 +201,139 @@
- + -

Class: FieldIlluminationKeyValues

-

URI: microscopemetrics_schema:FieldIlluminationKeyValues

+

Class: FieldIlluminationKeyMeasurements

+

URI: microscopemetrics_schema:FieldIlluminationKeyMeasurements

classDiagram - class FieldIlluminationKeyValues - KeyValues <|-- FieldIlluminationKeyValues + class FieldIlluminationKeyMeasurements + click FieldIlluminationKeyMeasurements href "../FieldIlluminationKeyMeasurements" + KeyMeasurements <|-- FieldIlluminationKeyMeasurements + click KeyMeasurements href "../KeyMeasurements" - FieldIlluminationKeyValues : bottom_center_intensity_mean + FieldIlluminationKeyMeasurements : bottom_center_intensity_mean - FieldIlluminationKeyValues : bottom_center_intensity_ratio + FieldIlluminationKeyMeasurements : bottom_center_intensity_ratio - FieldIlluminationKeyValues : bottom_left_intensity_mean + FieldIlluminationKeyMeasurements : bottom_left_intensity_mean - FieldIlluminationKeyValues : bottom_left_intensity_ratio + FieldIlluminationKeyMeasurements : bottom_left_intensity_ratio - FieldIlluminationKeyValues : bottom_right_intensity_mean + FieldIlluminationKeyMeasurements : bottom_right_intensity_mean - FieldIlluminationKeyValues : bottom_right_intensity_ratio + FieldIlluminationKeyMeasurements : bottom_right_intensity_ratio - FieldIlluminationKeyValues : center_fitted_distance_relative + FieldIlluminationKeyMeasurements : center_fitted_distance_relative - FieldIlluminationKeyValues : center_fitted_x + FieldIlluminationKeyMeasurements : center_fitted_x - FieldIlluminationKeyValues : center_fitted_x_relative + FieldIlluminationKeyMeasurements : center_fitted_x_relative - FieldIlluminationKeyValues : center_fitted_y + FieldIlluminationKeyMeasurements : center_fitted_y - FieldIlluminationKeyValues : center_fitted_y_relative + FieldIlluminationKeyMeasurements : center_fitted_y_relative - FieldIlluminationKeyValues : center_geometric_distance_relative + FieldIlluminationKeyMeasurements : center_geometric_distance_relative - FieldIlluminationKeyValues : center_geometric_x + FieldIlluminationKeyMeasurements : center_geometric_x - FieldIlluminationKeyValues : center_geometric_x_relative + FieldIlluminationKeyMeasurements : center_geometric_x_relative - FieldIlluminationKeyValues : center_geometric_y + FieldIlluminationKeyMeasurements : center_geometric_y - FieldIlluminationKeyValues : center_geometric_y_relative + FieldIlluminationKeyMeasurements : center_geometric_y_relative - FieldIlluminationKeyValues : center_of_mass_distance_relative + FieldIlluminationKeyMeasurements : center_of_mass_distance_relative - FieldIlluminationKeyValues : center_of_mass_x + FieldIlluminationKeyMeasurements : center_of_mass_x - FieldIlluminationKeyValues : center_of_mass_x_relative + FieldIlluminationKeyMeasurements : center_of_mass_x_relative - FieldIlluminationKeyValues : center_of_mass_y + FieldIlluminationKeyMeasurements : center_of_mass_y - FieldIlluminationKeyValues : center_of_mass_y_relative + FieldIlluminationKeyMeasurements : center_of_mass_y_relative - FieldIlluminationKeyValues : center_region_area_fraction + FieldIlluminationKeyMeasurements : center_region_area_fraction - FieldIlluminationKeyValues : center_region_intensity_fraction + FieldIlluminationKeyMeasurements : center_region_intensity_fraction - FieldIlluminationKeyValues : channel_name + FieldIlluminationKeyMeasurements : channel_id - FieldIlluminationKeyValues : data_reference + FieldIlluminationKeyMeasurements : channel_name - FieldIlluminationKeyValues --> DataReference : data_reference + FieldIlluminationKeyMeasurements : channel_nr - FieldIlluminationKeyValues : description + FieldIlluminationKeyMeasurements : data_reference - FieldIlluminationKeyValues : linked_references - FieldIlluminationKeyValues --> DataReference : linked_references - FieldIlluminationKeyValues : max_intensity - FieldIlluminationKeyValues : max_intensity_distance_relative + FieldIlluminationKeyMeasurements --> "0..1" DataReference : data_reference + click DataReference href "../DataReference" - FieldIlluminationKeyValues : max_intensity_pos_x - FieldIlluminationKeyValues : max_intensity_pos_x_relative + FieldIlluminationKeyMeasurements : description - FieldIlluminationKeyValues : max_intensity_pos_y + FieldIlluminationKeyMeasurements : image_id - FieldIlluminationKeyValues : max_intensity_pos_y_relative + FieldIlluminationKeyMeasurements : image_name - FieldIlluminationKeyValues : middle_center_intensity_mean + FieldIlluminationKeyMeasurements : linked_references - FieldIlluminationKeyValues : middle_center_intensity_ratio - FieldIlluminationKeyValues : middle_left_intensity_mean - FieldIlluminationKeyValues : middle_left_intensity_ratio - FieldIlluminationKeyValues : middle_right_intensity_mean + FieldIlluminationKeyMeasurements --> "*" DataReference : linked_references + click DataReference href "../DataReference" - FieldIlluminationKeyValues : middle_right_intensity_ratio - FieldIlluminationKeyValues : name + FieldIlluminationKeyMeasurements : max_intensity - FieldIlluminationKeyValues : top_center_intensity_mean + FieldIlluminationKeyMeasurements : max_intensity_distance_relative - FieldIlluminationKeyValues : top_center_intensity_ratio + FieldIlluminationKeyMeasurements : max_intensity_pos_x - FieldIlluminationKeyValues : top_left_intensity_mean + FieldIlluminationKeyMeasurements : max_intensity_pos_x_relative - FieldIlluminationKeyValues : top_left_intensity_ratio + FieldIlluminationKeyMeasurements : max_intensity_pos_y - FieldIlluminationKeyValues : top_right_intensity_mean + FieldIlluminationKeyMeasurements : max_intensity_pos_y_relative - FieldIlluminationKeyValues : top_right_intensity_ratio + FieldIlluminationKeyMeasurements : middle_center_intensity_mean + + FieldIlluminationKeyMeasurements : middle_center_intensity_ratio + + FieldIlluminationKeyMeasurements : middle_left_intensity_mean + + FieldIlluminationKeyMeasurements : middle_left_intensity_ratio + + FieldIlluminationKeyMeasurements : middle_right_intensity_mean + + FieldIlluminationKeyMeasurements : middle_right_intensity_ratio + + FieldIlluminationKeyMeasurements : name + + FieldIlluminationKeyMeasurements : table_data + + + + + FieldIlluminationKeyMeasurements --> "0..1" MetaObject : table_data + click MetaObject href "../MetaObject" + + + FieldIlluminationKeyMeasurements : top_center_intensity_mean + + FieldIlluminationKeyMeasurements : top_center_intensity_ratio + + FieldIlluminationKeyMeasurements : top_left_intensity_mean + + FieldIlluminationKeyMeasurements : top_left_intensity_ratio + + FieldIlluminationKeyMeasurements : top_right_intensity_mean + + FieldIlluminationKeyMeasurements : top_right_intensity_ratio
@@ -313,7 +342,10 @@

Inheritance

  • NamedObject
    • MetricsObject @@ -333,258 +365,288 @@

      Slots

      +image_name +*
      String +The name of the image where the measurement was taken +direct + + +image_id +*
      String +The id of the image where the measurement was taken +direct + + channel_name -0..*
      String +*
      String The channel name to which the measurements apply direct +channel_nr +*
      Integer +The channel number to which the measurements apply +direct + + +channel_id +*
      String +The channel id to which the measurements apply +direct + + center_region_intensity_fraction -0..*
      Float +*
      Float The fraction of the upper intensity range occupied by the center of illuminat... direct center_region_area_fraction -0..*
      Float +*
      Float The fraction of the area occupied by the center of illumination region direct center_of_mass_y -0..*
      Float +*
      Float The y coordinate of the center of mass of the center of illumination region direct center_of_mass_y_relative -0..*
      Float +*
      Float The relative y position of the center of mass of the center of illumination r... direct center_of_mass_x -0..*
      Float +*
      Float The x coordinate of the center of mass of the center of illumination region direct center_of_mass_x_relative -0..*
      Float +*
      Float The relative x position of the center of mass of the center of illumination r... direct center_of_mass_distance_relative -0..*
      Float +*
      Float The relative distance of the centers of mass to the center of the image direct center_geometric_y -0..*
      Float +*
      Float The y coordinate of the geometric center of the center of illumination region direct center_geometric_y_relative -0..*
      Float +*
      Float The relative y position of the geometric center of the center of illumination... direct center_geometric_x -0..*
      Float +*
      Float The x coordinate of the geometric center of the center of illumination region direct center_geometric_x_relative -0..*
      Float +*
      Float The relative x position of the geometric center of the center of illumination... direct center_geometric_distance_relative -0..*
      Float +*
      Float The relative distance of the geometric center to the center of the image direct center_fitted_y -0..*
      Float +*
      Float The y coordinate of the fitted center of illumination direct center_fitted_y_relative -0..*
      Float +*
      Float The relative y position of the fitted center of illumination direct center_fitted_x -0..*
      Float +*
      Float The x coordinate of the fitted center of illumination direct center_fitted_x_relative -0..*
      Float +*
      Float The relative x position of the fitted center of illumination direct center_fitted_distance_relative -0..*
      Float +*
      Float The relative distance of the fitted center of illumination to the center of t... direct max_intensity -0..*
      Float +*
      Float The maximum intensity of the center of illumination direct max_intensity_pos_y -0..*
      Float +*
      Float The y coordinate of the maximum intensity of the center of illumination direct max_intensity_pos_y_relative -0..*
      Float +*
      Float The relative y position of the maximum intensity of the center of illuminatio... direct max_intensity_pos_x -0..*
      Float +*
      Float The x coordinate of the maximum intensity of the center of illumination direct max_intensity_pos_x_relative -0..*
      Float +*
      Float The relative x position of the maximum intensity of the center of illuminatio... direct max_intensity_distance_relative -0..*
      Float +*
      Float The relative distance of the maximum intensity to the center of the image direct top_left_intensity_mean -0..*
      Float +*
      Float The mean intensity of the top-left corner of the image direct top_left_intensity_ratio -0..*
      Float +*
      Float The mean intensity of the top-left corner of the image divided by the maximu... direct top_center_intensity_mean -0..*
      Float +*
      Float The mean intensity of the top-center of the image direct top_center_intensity_ratio -0..*
      Float +*
      Float The mean intensity of the top-center of the image divided by the maximum int... direct top_right_intensity_mean -0..*
      Float +*
      Float The mean intensity of the top-right corner of the image direct top_right_intensity_ratio -0..*
      Float +*
      Float The mean intensity of the top-right corner of the image divided by the maxim... direct middle_left_intensity_mean -0..*
      Float +*
      Float The mean intensity of the middle-left of the image direct middle_left_intensity_ratio -0..*
      Float +*
      Float The mean intensity of the middle-left of the image divided by the maximum in... direct middle_center_intensity_mean -0..*
      Float +*
      Float The mean intensity of the middle-center of the image direct middle_center_intensity_ratio -0..*
      Float +*
      Float The mean intensity of the middle-center of the image divided by the maximum ... direct middle_right_intensity_mean -0..*
      Float +*
      Float The mean intensity of the middle-right of the image direct middle_right_intensity_ratio -0..*
      Float +*
      Float The mean intensity of the middle-right of the image divided by the maximum i... direct bottom_left_intensity_mean -0..*
      Float +*
      Float The mean intensity of the bottom-left of the image direct bottom_left_intensity_ratio -0..*
      Float +*
      Float The mean intensity of the bottom-left of the image divided by the maximum in... direct bottom_center_intensity_mean -0..*
      Float +*
      Float The mean intensity of the bottom-center of the image direct bottom_center_intensity_ratio -0..*
      Float +*
      Float The mean intensity of the bottom-center of the image divided by the maximum ... direct bottom_right_intensity_mean -0..*
      Float +*
      Float The mean intensity of the bottom-right of the image direct bottom_right_intensity_ratio -0..*
      Float +*
      Float The mean intensity of the bottom-right of the image divided by the maximum i... direct +table_data +0..1
      MetaObject +A non-required slot for non-serializable table data object +KeyMeasurements + + data_reference 0..1
      DataReference A reference to the data @@ -592,7 +654,7 @@

      Slots

      linked_references -0..*
      DataReference +*
      DataReference A list of linked references MetricsObject @@ -623,9 +685,9 @@

      Usages

      FieldIlluminationOutput -key_values +key_measurements range -FieldIlluminationKeyValues +FieldIlluminationKeyMeasurements @@ -645,11 +707,11 @@

      Mappings

      self -microscopemetrics_schema:FieldIlluminationKeyValues +microscopemetrics_schema:FieldIlluminationKeyMeasurements native -microscopemetrics_schema:FieldIlluminationKeyValues +microscopemetrics_schema:FieldIlluminationKeyMeasurements @@ -657,11 +719,15 @@

      LinkML Source

      Direct

      -
      name: FieldIlluminationKeyValues
+
      name: FieldIlluminationKeyMeasurements
 from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: KeyValues
+is_a: KeyMeasurements
 slots:
+- image_name
+- image_id
 - channel_name
+- channel_nr
+- channel_id
 - center_region_intensity_fraction
 - center_region_area_fraction
 - center_of_mass_y
@@ -708,21 +774,69 @@ 
      Direct

      Induced

      -
      name: FieldIlluminationKeyValues
+
      name: FieldIlluminationKeyMeasurements
 from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: KeyValues
+is_a: KeyMeasurements
 attributes:
+  image_name:
+    name: image_name
+    description: The name of the image where the measurement was taken
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+    rank: 1000
+    alias: image_name
+    owner: FieldIlluminationKeyMeasurements
+    domain_of:
+    - FieldIlluminationKeyMeasurements
+    range: string
+    multivalued: true
+  image_id:
+    name: image_id
+    description: The id of the image where the measurement was taken. If images are
+      originary in OMERO this is the image_id.
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+    rank: 1000
+    alias: image_id
+    owner: FieldIlluminationKeyMeasurements
+    domain_of:
+    - FieldIlluminationKeyMeasurements
+    range: string
+    multivalued: true
   channel_name:
     name: channel_name
     description: The channel name to which the measurements apply
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: channel_name
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
+    - PSFBeadsKeyMeasurements
     range: string
+    multivalued: true
+  channel_nr:
+    name: channel_nr
+    description: The channel number to which the measurements apply
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+    rank: 1000
+    alias: channel_nr
+    owner: FieldIlluminationKeyMeasurements
+    domain_of:
+    - FieldIlluminationKeyMeasurements
+    - PSFBeadsKeyMeasurements
+    range: integer
+    multivalued: true
+    minimum_value: 0
+  channel_id:
+    name: channel_id
+    description: The channel id to which the measurements apply
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+    rank: 1000
+    alias: channel_id
+    owner: FieldIlluminationKeyMeasurements
+    domain_of:
+    - FieldIlluminationKeyMeasurements
+    range: string
+    multivalued: true
   center_region_intensity_fraction:
     name: center_region_intensity_fraction
     description: The fraction of the upper intensity range occupied by the center
@@ -732,12 +846,12 @@ 
      Induced
      
       One value per channel.
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: center_region_intensity_fraction
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
     minimum_value: 0.0
     maximum_value: 1.0
   center_region_area_fraction:
@@ -747,12 +861,12 @@ 
      Induced
      
       illumination occupies 10% of the area of the image. One value per channel.
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: center_region_area_fraction
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
     minimum_value: 0.0
     maximum_value: 1.0
   center_of_mass_y:
@@ -761,12 +875,12 @@ 
      Induced
      
       region. In pixels. One value per channel.
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: center_of_mass_y
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   center_of_mass_y_relative:
     name: center_of_mass_y_relative
     description: The relative y position of the center of mass of the center of illumination
@@ -774,12 +888,12 @@ 
      Induced
      
       is center and 1.0 is lower edge. One value per channel.
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: center_of_mass_y_relative
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
     minimum_value: -1.0
     maximum_value: 1.0
   center_of_mass_x:
@@ -788,12 +902,12 @@ 
      Induced
      
       region. In pixels. One value per channel.
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: center_of_mass_x
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   center_of_mass_x_relative:
     name: center_of_mass_x_relative
     description: The relative x position of the center of mass of the center of illumination
@@ -801,12 +915,12 @@ 
      Induced
      
       is center and 1.0 is right edge. One value per channel.
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: center_of_mass_x_relative
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
     minimum_value: -1.0
     maximum_value: 1.0
   center_of_mass_distance_relative:
@@ -816,12 +930,12 @@ 
      Induced
      
       at a distance equal to the the corner of the image. One value per channel.
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: center_of_mass_distance_relative
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
     minimum_value: 0.0
     maximum_value: 1.0
   center_geometric_y:
@@ -830,12 +944,12 @@ 
      Induced
      
       region. In pixels. One value per channel.
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: center_geometric_y
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   center_geometric_y_relative:
     name: center_geometric_y_relative
     description: The relative y position of the geometric center of the center of
@@ -843,12 +957,12 @@ 
      Induced
      
       edge, 0.0 is center and 1.0 is lower edge. One value per channel.
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: center_geometric_y_relative
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
     minimum_value: -1.0
     maximum_value: 1.0
   center_geometric_x:
@@ -857,12 +971,12 @@ 
      Induced
      
       region. In pixels
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: center_geometric_x
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   center_geometric_x_relative:
     name: center_geometric_x_relative
     description: The relative x position of the geometric center of the center of
@@ -870,12 +984,12 @@ 
      Induced
      
       edge, 0.0 is center and 1.0 is right edge.
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: center_geometric_x_relative
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
     minimum_value: -1.0
     maximum_value: 1.0
   center_geometric_distance_relative:
@@ -885,12 +999,12 @@ 
      Induced
      
       at a distance equal to the the corner of the image.
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: center_geometric_distance_relative
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
     minimum_value: 0.0
     maximum_value: 1.0
   center_fitted_y:
@@ -898,12 +1012,12 @@ 
      Induced
      
     description: The y coordinate of the fitted center of illumination. In pixels
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: center_fitted_y
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   center_fitted_y_relative:
     name: center_fitted_y_relative
     description: The relative y position of the fitted center of illumination.  Relative
@@ -911,12 +1025,12 @@ 
      Induced
      
       is lower edge.
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: center_fitted_y_relative
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
     minimum_value: -1.0
     maximum_value: 1.0
   center_fitted_x:
@@ -924,12 +1038,12 @@ 
      Induced
      
     description: The x coordinate of the fitted center of illumination. In pixels
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: center_fitted_x
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   center_fitted_x_relative:
     name: center_fitted_x_relative
     description: The relative x position of the fitted center of illumination.  Relative
@@ -937,12 +1051,12 @@ 
      Induced
      
       is right edge.
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: center_fitted_x_relative
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
     minimum_value: -1.0
     maximum_value: 1.0
   center_fitted_distance_relative:
@@ -952,12 +1066,12 @@ 
      Induced
      
       and 1.0 at a distance equal to the the corner of the image.
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: center_fitted_distance_relative
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
     minimum_value: 0.0
     maximum_value: 1.0
   max_intensity:
@@ -965,24 +1079,24 @@ 
      Induced
      
     description: The maximum intensity of the center of illumination
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: max_intensity
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   max_intensity_pos_y:
     name: max_intensity_pos_y
     description: The y coordinate of the maximum intensity of the center of illumination.
       In pixels
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: max_intensity_pos_y
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   max_intensity_pos_y_relative:
     name: max_intensity_pos_y_relative
     description: The relative y position of the maximum intensity of the center of
@@ -990,12 +1104,12 @@ 
      Induced
      
       0.0 is center and 1.0 is lower edge.
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: max_intensity_pos_y_relative
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
     minimum_value: -1.0
     maximum_value: 1.0
   max_intensity_pos_x:
@@ -1004,12 +1118,12 @@ 
      Induced
      
       In pixels
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: max_intensity_pos_x
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   max_intensity_pos_x_relative:
     name: max_intensity_pos_x_relative
     description: The relative x position of the maximum intensity of the center of
@@ -1017,12 +1131,12 @@ 
      Induced
      
       0.0 is center and 1.0 is right edge.
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: max_intensity_pos_x_relative
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
     minimum_value: -1.0
     maximum_value: 1.0
   max_intensity_distance_relative:
@@ -1032,12 +1146,12 @@ 
      Induced
      
       at a distance equal to the the corner of the image.
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: max_intensity_distance_relative
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
     minimum_value: 0.0
     maximum_value: 1.0
   top_left_intensity_mean:
@@ -1045,232 +1159,245 @@ 
      Induced
      
     description: The mean intensity of the top-left corner of the image
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: top_left_intensity_mean
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   top_left_intensity_ratio:
     name: top_left_intensity_ratio
     description: The mean intensity of the top-left corner of the image  divided by
       the maximum intensity of the center of illumination
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: top_left_intensity_ratio
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   top_center_intensity_mean:
     name: top_center_intensity_mean
     description: The mean intensity of the top-center of the image
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: top_center_intensity_mean
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   top_center_intensity_ratio:
     name: top_center_intensity_ratio
     description: The mean intensity of the top-center of the image  divided by the
       maximum intensity of the center of illumination
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: top_center_intensity_ratio
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   top_right_intensity_mean:
     name: top_right_intensity_mean
     description: The mean intensity of the top-right corner of the image
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: top_right_intensity_mean
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   top_right_intensity_ratio:
     name: top_right_intensity_ratio
     description: The mean intensity of the top-right corner of the image  divided
       by the maximum intensity of the center of illumination
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: top_right_intensity_ratio
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   middle_left_intensity_mean:
     name: middle_left_intensity_mean
     description: The mean intensity of the middle-left of the image
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: middle_left_intensity_mean
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   middle_left_intensity_ratio:
     name: middle_left_intensity_ratio
     description: The mean intensity of the middle-left of the image  divided by the
       maximum intensity of the center of illumination
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: middle_left_intensity_ratio
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   middle_center_intensity_mean:
     name: middle_center_intensity_mean
     description: The mean intensity of the middle-center of the image
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: middle_center_intensity_mean
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   middle_center_intensity_ratio:
     name: middle_center_intensity_ratio
     description: The mean intensity of the middle-center of the image  divided by
       the maximum intensity of the center of illumination
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: middle_center_intensity_ratio
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   middle_right_intensity_mean:
     name: middle_right_intensity_mean
     description: The mean intensity of the middle-right of the image
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: middle_right_intensity_mean
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   middle_right_intensity_ratio:
     name: middle_right_intensity_ratio
     description: The mean intensity of the middle-right of the image  divided by the
       maximum intensity of the center of illumination
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: middle_right_intensity_ratio
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   bottom_left_intensity_mean:
     name: bottom_left_intensity_mean
     description: The mean intensity of the bottom-left of the image
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: bottom_left_intensity_mean
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   bottom_left_intensity_ratio:
     name: bottom_left_intensity_ratio
     description: The mean intensity of the bottom-left of the image  divided by the
       maximum intensity of the center of illumination
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: bottom_left_intensity_ratio
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   bottom_center_intensity_mean:
     name: bottom_center_intensity_mean
     description: The mean intensity of the bottom-center of the image
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: bottom_center_intensity_mean
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   bottom_center_intensity_ratio:
     name: bottom_center_intensity_ratio
     description: The mean intensity of the bottom-center of the image  divided by
       the maximum intensity of the center of illumination
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: bottom_center_intensity_ratio
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   bottom_right_intensity_mean:
     name: bottom_right_intensity_mean
     description: The mean intensity of the bottom-right of the image
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: bottom_right_intensity_mean
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
   bottom_right_intensity_ratio:
     name: bottom_right_intensity_ratio
     description: The mean intensity of the bottom-right of the image  divided by the
       maximum intensity of the center of illumination
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: true
     alias: bottom_right_intensity_ratio
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
-    - FieldIlluminationKeyValues
+    - FieldIlluminationKeyMeasurements
     range: float
+    multivalued: true
+  table_data:
+    name: table_data
+    description: A non-required slot for non-serializable table data object
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
+    rank: 1000
+    alias: table_data
+    owner: FieldIlluminationKeyMeasurements
+    domain_of:
+    - KeyMeasurements
+    - Table
+    range: MetaObject
+    required: false
+    multivalued: false
   data_reference:
     name: data_reference
     description: A reference to the data
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
     rank: 1000
-    multivalued: false
     alias: data_reference
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
     - MetricsObject
     range: DataReference
     required: false
+    multivalued: false
   linked_references:
     name: linked_references
     description: A list of linked references
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
     rank: 1000
-    multivalued: true
     alias: linked_references
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
     - MetricsObject
     range: DataReference
     required: false
+    multivalued: true
     inlined: true
     inlined_as_list: true
   name:
@@ -1278,27 +1405,27 @@ 
      Induced
      
     description: The human readable name of an entity
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: false
     alias: name
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
     - NamedObject
     - Experimenter
     range: string
     required: false
+    multivalued: false
   description:
     name: description
     description: A human readable description of an entity
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: false
     alias: description
-    owner: FieldIlluminationKeyValues
+    owner: FieldIlluminationKeyMeasurements
     domain_of:
     - NamedObject
     - Tag
     range: string
     required: false
+    multivalued: false
      @@ -1327,5 +1454,7 @@

      Induced

    • - + \ No newline at end of file diff --git a/FieldIlluminationOutput/index.html b/FieldIlluminationOutput/index.html index 47a7d9cd..2d451745 100644 --- a/FieldIlluminationOutput/index.html +++ b/FieldIlluminationOutput/index.html @@ -7,7 +7,7 @@ - + Class: FieldIlluminationOutput - microscopemetrics-schema @@ -208,21 +208,38 @@

    Class: FieldIlluminationOutput

    URI: microscopemetrics_schema:FieldIlluminationOutput

    classDiagram class FieldIlluminationOutput + click FieldIlluminationOutput href "../FieldIlluminationOutput" MetricsOutput <|-- FieldIlluminationOutput + click MetricsOutput href "../MetricsOutput" FieldIlluminationOutput : comment - FieldIlluminationOutput --> Comment : comment + + + + FieldIlluminationOutput --> "0..1" Comment : comment + click Comment href "../Comment" + FieldIlluminationOutput : errors FieldIlluminationOutput : intensity_profiles - FieldIlluminationOutput --> Table : intensity_profiles - FieldIlluminationOutput : key_values - FieldIlluminationOutput --> FieldIlluminationKeyValues : key_values + + FieldIlluminationOutput --> "*" Table : intensity_profiles + click Table href "../Table" + + + FieldIlluminationOutput : key_measurements + + + + + FieldIlluminationOutput --> "0..1" FieldIlluminationKeyMeasurements : key_measurements + click FieldIlluminationKeyMeasurements href "../FieldIlluminationKeyMeasurements" + FieldIlluminationOutput : processing_application @@ -236,31 +253,70 @@

    Class: FieldIlluminationOutput

    FieldIlluminationOutput : roi_center_region - FieldIlluminationOutput --> Roi : roi_center_region + + + + FieldIlluminationOutput --> "*" Roi : roi_center_region + click Roi href "../Roi" + FieldIlluminationOutput : roi_centers_fitted - FieldIlluminationOutput --> Roi : roi_centers_fitted + + + + FieldIlluminationOutput --> "*" Roi : roi_centers_fitted + click Roi href "../Roi" + FieldIlluminationOutput : roi_centers_geometric - FieldIlluminationOutput --> Roi : roi_centers_geometric + + + + FieldIlluminationOutput --> "*" Roi : roi_centers_geometric + click Roi href "../Roi" + FieldIlluminationOutput : roi_centers_max_intensity - FieldIlluminationOutput --> Roi : roi_centers_max_intensity + + + + FieldIlluminationOutput --> "*" Roi : roi_centers_max_intensity + click Roi href "../Roi" + FieldIlluminationOutput : roi_centers_of_mass - FieldIlluminationOutput --> Roi : roi_centers_of_mass + + + + FieldIlluminationOutput --> "*" Roi : roi_centers_of_mass + click Roi href "../Roi" + FieldIlluminationOutput : roi_corners - FieldIlluminationOutput --> Roi : roi_corners + + + + FieldIlluminationOutput --> "0..1" Roi : roi_corners + click Roi href "../Roi" + FieldIlluminationOutput : roi_profiles - FieldIlluminationOutput --> Roi : roi_profiles + + + + FieldIlluminationOutput --> "*" Roi : roi_profiles + click Roi href "../Roi" + + + FieldIlluminationOutput : validated + + FieldIlluminationOutput : validation_datetime FieldIlluminationOutput : warnings @@ -285,20 +341,20 @@

    Slots

    -key_values -0..1
    FieldIlluminationKeyValues +key_measurements +0..1
    FieldIlluminationKeyMeasurements Key-Value pairs containing the Key measurements for the field illumination an... direct intensity_profiles -0..*
    Table +*
    Table Intensity profiles for the field illumination analysis in the different direc... direct roi_profiles -0..*
    Roi +*
    Roi line ROIs used to compute the intensity profiles direct @@ -310,31 +366,31 @@

    Slots

    roi_centers_of_mass -0..*
    Roi +*
    Roi Point ROIs marking the center of mass of the area of maximum illumination direct roi_centers_geometric -0..*
    Roi +*
    Roi Point ROIs marking the geometric center of the area of maximum illumination direct roi_centers_fitted -0..*
    Roi +*
    Roi Point ROIs marking the fitted center of the area of maximum illumination direct roi_centers_max_intensity -0..*
    Roi +*
    Roi Point ROIs marking the maximum intensity of the area of maximum illumination direct roi_center_region -0..*
    Roi +*
    Roi Mask ROIs marking the area of maximum illumination direct @@ -352,13 +408,13 @@

    Slots

    processing_entity -0..*
    String +*
    String The entity that processed the dataset MetricsOutput processing_datetime -1..1
    datetime +1
    datetime The datetime of the processing by microscope-metrics MetricsOutput @@ -370,17 +426,29 @@

    Slots

    warnings -0..*
    String +*
    String The warnings of the processing by microscope-metrics MetricsOutput errors -0..*
    String +*
    String The errors of the processing by microscope-metrics MetricsOutput +validated +1
    Boolean +Has the dataset been validated by a human +MetricsOutput + + +validation_datetime +0..1
    datetime +The datetime of the validation +MetricsOutput + + comment 0..1
    Comment A human readable comment about the dataset @@ -439,100 +507,99 @@

    Direct

    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema is_a: MetricsOutput attributes: - key_values: - name: key_values + key_measurements: + name: key_measurements description: Key-Value pairs containing the Key measurements for the field illumination analysis - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema rank: 1000 - multivalued: false domain_of: - FieldIlluminationOutput - PSFBeadsOutput - range: FieldIlluminationKeyValues + range: FieldIlluminationKeyMeasurements + multivalued: false intensity_profiles: name: intensity_profiles description: Intensity profiles for the field illumination analysis in the different directions - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema rank: 1000 - multivalued: true domain_of: - FieldIlluminationOutput - - ArgolightEOutput range: Table + multivalued: true inlined: true inlined_as_list: true roi_profiles: name: roi_profiles description: line ROIs used to compute the intensity profiles - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema rank: 1000 - multivalued: true domain_of: - FieldIlluminationOutput range: Roi + multivalued: true roi_corners: name: roi_corners description: Rectangular ROIs used to compute the corner intensities. The sama ROI is assigned to multiple images. - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema rank: 1000 - multivalued: false domain_of: - FieldIlluminationOutput range: Roi + multivalued: false roi_centers_of_mass: name: roi_centers_of_mass description: Point ROIs marking the center of mass of the area of maximum illumination. When the image is very flat, the 99 percentile is used instead. One point per channel. - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema rank: 1000 - multivalued: true domain_of: - FieldIlluminationOutput range: Roi + multivalued: true roi_centers_geometric: name: roi_centers_geometric description: Point ROIs marking the geometric center of the area of maximum illumination. One point per channel. - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema rank: 1000 - multivalued: true domain_of: - FieldIlluminationOutput range: Roi + multivalued: true roi_centers_fitted: name: roi_centers_fitted description: Point ROIs marking the fitted center of the area of maximum illumination. One point per channel. - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema rank: 1000 - multivalued: true domain_of: - FieldIlluminationOutput range: Roi + multivalued: true roi_centers_max_intensity: name: roi_centers_max_intensity description: Point ROIs marking the maximum intensity of the area of maximum illumination. One point per channel. - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema rank: 1000 - multivalued: true domain_of: - FieldIlluminationOutput range: Roi + multivalued: true roi_center_region: name: roi_center_region description: Mask ROIs marking the area of maximum illumination. One mask per channel. - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema rank: 1000 - multivalued: true domain_of: - FieldIlluminationOutput range: Roi + multivalued: true     @@ -542,214 +609,238 @@

    Induced

    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema is_a: MetricsOutput attributes: - key_values: - name: key_values + key_measurements: + name: key_measurements description: Key-Value pairs containing the Key measurements for the field illumination analysis - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema rank: 1000 - multivalued: false - alias: key_values + alias: key_measurements owner: FieldIlluminationOutput domain_of: - FieldIlluminationOutput - PSFBeadsOutput - range: FieldIlluminationKeyValues + range: FieldIlluminationKeyMeasurements + multivalued: false intensity_profiles: name: intensity_profiles description: Intensity profiles for the field illumination analysis in the different directions - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema rank: 1000 - multivalued: true alias: intensity_profiles owner: FieldIlluminationOutput domain_of: - FieldIlluminationOutput - - ArgolightEOutput range: Table + multivalued: true inlined: true inlined_as_list: true roi_profiles: name: roi_profiles description: line ROIs used to compute the intensity profiles - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema rank: 1000 - multivalued: true alias: roi_profiles owner: FieldIlluminationOutput domain_of: - FieldIlluminationOutput range: Roi + multivalued: true roi_corners: name: roi_corners description: Rectangular ROIs used to compute the corner intensities. The sama ROI is assigned to multiple images. - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema rank: 1000 - multivalued: false alias: roi_corners owner: FieldIlluminationOutput domain_of: - FieldIlluminationOutput range: Roi + multivalued: false roi_centers_of_mass: name: roi_centers_of_mass description: Point ROIs marking the center of mass of the area of maximum illumination. When the image is very flat, the 99 percentile is used instead. One point per channel. - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema rank: 1000 - multivalued: true alias: roi_centers_of_mass owner: FieldIlluminationOutput domain_of: - FieldIlluminationOutput range: Roi + multivalued: true roi_centers_geometric: name: roi_centers_geometric description: Point ROIs marking the geometric center of the area of maximum illumination. One point per channel. - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema rank: 1000 - multivalued: true alias: roi_centers_geometric owner: FieldIlluminationOutput domain_of: - FieldIlluminationOutput range: Roi + multivalued: true roi_centers_fitted: name: roi_centers_fitted description: Point ROIs marking the fitted center of the area of maximum illumination. One point per channel. - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema rank: 1000 - multivalued: true alias: roi_centers_fitted owner: FieldIlluminationOutput domain_of: - FieldIlluminationOutput range: Roi + multivalued: true roi_centers_max_intensity: name: roi_centers_max_intensity description: Point ROIs marking the maximum intensity of the area of maximum illumination. One point per channel. - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema rank: 1000 - multivalued: true alias: roi_centers_max_intensity owner: FieldIlluminationOutput domain_of: - FieldIlluminationOutput range: Roi + multivalued: true roi_center_region: name: roi_center_region description: Mask ROIs marking the area of maximum illumination. One mask per channel. - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/field_illumination_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/field_illumination_schema rank: 1000 - multivalued: true alias: roi_center_region owner: FieldIlluminationOutput domain_of: - FieldIlluminationOutput range: Roi + multivalued: true processing_application: name: processing_application description: The application used to process the dataset from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: processing_application owner: FieldIlluminationOutput domain_of: - MetricsOutput range: string required: true + multivalued: true processing_version: name: processing_version description: The version of the application used to process the dataset from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: processing_version owner: FieldIlluminationOutput domain_of: - MetricsOutput range: string required: true + multivalued: true processing_entity: name: processing_entity description: The entity that processed the dataset from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: processing_entity owner: FieldIlluminationOutput domain_of: - MetricsOutput range: string required: false + multivalued: true processing_datetime: name: processing_datetime description: The datetime of the processing by microscope-metrics from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: processing_datetime owner: FieldIlluminationOutput domain_of: - MetricsOutput range: datetime required: true + multivalued: false processing_log: name: processing_log description: The log of the processing by microscope-metrics from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: processing_log owner: FieldIlluminationOutput domain_of: - MetricsOutput range: string required: false + multivalued: false warnings: name: warnings description: The warnings of the processing by microscope-metrics from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: warnings owner: FieldIlluminationOutput domain_of: - MetricsOutput range: string required: false + multivalued: true errors: name: errors description: The errors of the processing by microscope-metrics from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: errors owner: FieldIlluminationOutput domain_of: - MetricsOutput range: string required: false + multivalued: true + validated: + name: validated + description: Has the dataset been validated by a human + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema + rank: 1000 + ifabsent: 'False' + alias: validated + owner: FieldIlluminationOutput + domain_of: + - MetricsOutput + range: boolean + required: true + multivalued: false + validation_datetime: + name: validation_datetime + description: The datetime of the validation + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema + rank: 1000 + alias: validation_datetime + owner: FieldIlluminationOutput + domain_of: + - MetricsOutput + range: datetime + required: false + multivalued: false comment: name: comment description: A human readable comment about the dataset from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: comment owner: FieldIlluminationOutput domain_of: - MetricsOutput range: Comment required: false + multivalued: false     @@ -778,5 +869,7 @@

    Induced

    - + \ No newline at end of file diff --git a/Float/index.html b/Float/index.html index 3f28fadf..e7142abe 100644 --- a/Float/index.html +++ b/Float/index.html @@ -11,7 +11,7 @@ - + diff --git a/FluorescentHomogeneousThickField/index.html b/FluorescentHomogeneousThickField/index.html new file mode 100644 index 00000000..78814b67 --- /dev/null +++ b/FluorescentHomogeneousThickField/index.html @@ -0,0 +1,403 @@ + + + + + + + + + + +Class: FluorescentHomogeneousThickField - microscopemetrics-schema + + + + + + + + + + + +
    + + Skip to content + +
    +
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    +
    + +
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    + +
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    + + + +

    Class: FluorescentHomogeneousThickField

    +

    An homogeneous field with a fluorescent thick sample. Similar to the Chroma slides.

    +

    URI: microscopemetrics_schema:FluorescentHomogeneousThickField

    +
    classDiagram + class FluorescentHomogeneousThickField + click FluorescentHomogeneousThickField href "../FluorescentHomogeneousThickField" + HomogeneousField <|-- FluorescentHomogeneousThickField + click HomogeneousField href "../HomogeneousField" + + FluorescentHomogeneousThickField : description + + FluorescentHomogeneousThickField : manufacturer + + FluorescentHomogeneousThickField : name + + FluorescentHomogeneousThickField : protocol + + + + + FluorescentHomogeneousThickField --> "1" Protocol : protocol + click Protocol href "../Protocol" + + + +
    +

    Inheritance

    + +

    Slots

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    NameCardinality and RangeDescriptionInheritance
    protocol1
    Protocol    		The protocol used to prepare the sampleSample
    manufacturer0..1
    String    		The manufacturer of the beadsSample
    name0..1
    String    		The human readable name of an entityNamedObject
    description0..1
    String    		A human readable description of an entityNamedObject
    +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
      • +
    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfmicroscopemetrics_schema:FluorescentHomogeneousThickField
    nativemicroscopemetrics_schema:FluorescentHomogeneousThickField
    +

    LinkML Source

    + +

    Direct

    +
    +
    name: FluorescentHomogeneousThickField
+description: An homogeneous field with a fluorescent thick sample. Similar to the
+  Chroma slides.
+from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+is_a: HomogeneousField
+
+
    +
    +

    Induced

    +
    +
    name: FluorescentHomogeneousThickField
+description: An homogeneous field with a fluorescent thick sample. Similar to the
+  Chroma slides.
+from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+is_a: HomogeneousField
+attributes:
+  protocol:
+    name: protocol
+    description: The protocol used to prepare the sample
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
+    rank: 1000
+    alias: protocol
+    owner: FluorescentHomogeneousThickField
+    domain_of:
+    - Sample
+    range: Protocol
+    required: true
+    multivalued: false
+    inlined: false
+  manufacturer:
+    name: manufacturer
+    description: The manufacturer of the beads.
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
+    alias: manufacturer
+    owner: FluorescentHomogeneousThickField
+    domain_of:
+    - Microscope
+    - Sample
+    range: string
+    required: false
+  name:
+    name: name
+    description: The human readable name of an entity
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+    rank: 1000
+    alias: name
+    owner: FluorescentHomogeneousThickField
+    domain_of:
+    - NamedObject
+    - Experimenter
+    range: string
+    required: false
+    multivalued: false
+  description:
+    name: description
+    description: A human readable description of an entity
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+    rank: 1000
+    alias: description
+    owner: FluorescentHomogeneousThickField
+    domain_of:
+    - NamedObject
+    - Tag
+    range: string
+    required: false
+    multivalued: false
+
+
    +
    +
    +
    + +
    +
    + +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/FluorescentHomogeneousThinField/index.html b/FluorescentHomogeneousThinField/index.html new file mode 100644 index 00000000..b0f9df9c --- /dev/null +++ b/FluorescentHomogeneousThinField/index.html @@ -0,0 +1,403 @@ + + + + + + + + + + +Class: FluorescentHomogeneousThinField - microscopemetrics-schema + + + + + + + + + + + +
    + + Skip to content + +
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    + +
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    +
    + + + +

    Class: FluorescentHomogeneousThinField

    +

    An homogeneous field with a fluorescent thin sample. Similar to a dye thin layer.

    +

    URI: microscopemetrics_schema:FluorescentHomogeneousThinField

    +
    classDiagram + class FluorescentHomogeneousThinField + click FluorescentHomogeneousThinField href "../FluorescentHomogeneousThinField" + HomogeneousField <|-- FluorescentHomogeneousThinField + click HomogeneousField href "../HomogeneousField" + + FluorescentHomogeneousThinField : description + + FluorescentHomogeneousThinField : manufacturer + + FluorescentHomogeneousThinField : name + + FluorescentHomogeneousThinField : protocol + + + + + FluorescentHomogeneousThinField --> "1" Protocol : protocol + click Protocol href "../Protocol" + + + +
    +

    Inheritance

    + +

    Slots

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    NameCardinality and RangeDescriptionInheritance
    protocol1
    Protocol    		The protocol used to prepare the sampleSample
    manufacturer0..1
    String    		The manufacturer of the beadsSample
    name0..1
    String    		The human readable name of an entityNamedObject
    description0..1
    String    		A human readable description of an entityNamedObject
    +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
      • +
    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfmicroscopemetrics_schema:FluorescentHomogeneousThinField
    nativemicroscopemetrics_schema:FluorescentHomogeneousThinField
    +

    LinkML Source

    + +

    Direct

    +
    +
    name: FluorescentHomogeneousThinField
+description: An homogeneous field with a fluorescent thin sample. Similar to a dye
+  thin layer.
+from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+is_a: HomogeneousField
+
+
    +
    +

    Induced

    +
    +
    name: FluorescentHomogeneousThinField
+description: An homogeneous field with a fluorescent thin sample. Similar to a dye
+  thin layer.
+from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+is_a: HomogeneousField
+attributes:
+  protocol:
+    name: protocol
+    description: The protocol used to prepare the sample
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
+    rank: 1000
+    alias: protocol
+    owner: FluorescentHomogeneousThinField
+    domain_of:
+    - Sample
+    range: Protocol
+    required: true
+    multivalued: false
+    inlined: false
+  manufacturer:
+    name: manufacturer
+    description: The manufacturer of the beads.
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
+    alias: manufacturer
+    owner: FluorescentHomogeneousThinField
+    domain_of:
+    - Microscope
+    - Sample
+    range: string
+    required: false
+  name:
+    name: name
+    description: The human readable name of an entity
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+    rank: 1000
+    alias: name
+    owner: FluorescentHomogeneousThinField
+    domain_of:
+    - NamedObject
+    - Experimenter
+    range: string
+    required: false
+    multivalued: false
+  description:
+    name: description
+    description: A human readable description of an entity
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+    rank: 1000
+    alias: description
+    owner: FluorescentHomogeneousThinField
+    domain_of:
+    - NamedObject
+    - Tag
+    range: string
+    required: false
+    multivalued: false
+
+
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    + + + + \ No newline at end of file diff --git a/HarmonizedMetricsDatasetCollection/index.html b/HarmonizedMetricsDatasetCollection/index.html index ccb099c0..9da90d89 100644 --- a/HarmonizedMetricsDatasetCollection/index.html +++ b/HarmonizedMetricsDatasetCollection/index.html @@ -7,7 +7,7 @@ - + Class: HarmonizedMetricsDatasetCollection - microscopemetrics-schema @@ -204,23 +204,40 @@

    Class: HarmonizedMetricsDatase

    URI: microscopemetrics_schema:HarmonizedMetricsDatasetCollection

    classDiagram class HarmonizedMetricsDatasetCollection + click HarmonizedMetricsDatasetCollection href "../HarmonizedMetricsDatasetCollection" MetricsDatasetCollection <|-- HarmonizedMetricsDatasetCollection + click MetricsDatasetCollection href "../MetricsDatasetCollection" HarmonizedMetricsDatasetCollection : data_reference - HarmonizedMetricsDatasetCollection --> DataReference : data_reference + + + + HarmonizedMetricsDatasetCollection --> "0..1" DataReference : data_reference + click DataReference href "../DataReference" + HarmonizedMetricsDatasetCollection : dataset_class HarmonizedMetricsDatasetCollection : datasets - HarmonizedMetricsDatasetCollection --> MetricsDataset : datasets + + + + HarmonizedMetricsDatasetCollection --> "*" MetricsDataset : datasets + click MetricsDataset href "../MetricsDataset" + HarmonizedMetricsDatasetCollection : description HarmonizedMetricsDatasetCollection : linked_references - HarmonizedMetricsDatasetCollection --> DataReference : linked_references + + + + HarmonizedMetricsDatasetCollection --> "*" DataReference : linked_references + click DataReference href "../DataReference" + HarmonizedMetricsDatasetCollection : name @@ -252,13 +269,13 @@

    Slots

    dataset_class -1..1
    String +1
    String The class of the datasets in the collection direct datasets -0..*
    MetricsDataset +*
    MetricsDataset The datasets of the collection MetricsDatasetCollection @@ -270,7 +287,7 @@

    Slots

    linked_references -0..*
    DataReference +*
    DataReference A list of linked references MetricsObject @@ -327,11 +344,11 @@

    Direct

    description: The class of the datasets in the collection from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - HarmonizedMetricsDatasetCollection range: string required: true + multivalued: false @@ -348,24 +365,24 @@

    Induced

    description: The class of the datasets in the collection from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: dataset_class owner: HarmonizedMetricsDatasetCollection domain_of: - HarmonizedMetricsDatasetCollection range: string required: true + multivalued: false datasets: name: datasets description: The datasets of the collection from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: datasets owner: HarmonizedMetricsDatasetCollection domain_of: - MetricsDatasetCollection range: MetricsDataset + multivalued: true inlined: true inlined_as_list: true data_reference: @@ -373,25 +390,25 @@

    Induced

    description: A reference to the data from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: data_reference owner: HarmonizedMetricsDatasetCollection domain_of: - MetricsObject range: DataReference required: false + multivalued: false linked_references: name: linked_references description: A list of linked references from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: linked_references owner: HarmonizedMetricsDatasetCollection domain_of: - MetricsObject range: DataReference required: false + multivalued: true inlined: true inlined_as_list: true name: @@ -399,7 +416,6 @@

    Induced

    description: The human readable name of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: name owner: HarmonizedMetricsDatasetCollection domain_of: @@ -407,12 +423,12 @@

    Induced

    - Experimenter range: string required: false + multivalued: false description: name: description description: A human readable description of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: description owner: HarmonizedMetricsDatasetCollection domain_of: @@ -420,6 +436,7 @@

    Induced

    - Tag range: string required: false + multivalued: false @@ -448,5 +465,7 @@

    Induced

    - + \ No newline at end of file diff --git a/HomogeneousField/index.html b/HomogeneousField/index.html new file mode 100644 index 00000000..3e81c6f8 --- /dev/null +++ b/HomogeneousField/index.html @@ -0,0 +1,438 @@ + + + + + + + + + + +Class: HomogeneousField - microscopemetrics-schema + + + + + + + + + + + +
    + + Skip to content + +
    +
    +
    +
    + +
    +
    +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    +
    + +
    +
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    +
    +
    + + + +

    Class: HomogeneousField

    +

    An homogeneous field.

    +
      +
    • NOTE: this is an abstract class and should not be instantiated directly
      • +
    +

    URI: microscopemetrics_schema:HomogeneousField

    +
    classDiagram + class HomogeneousField + click HomogeneousField href "../HomogeneousField" + Sample <|-- HomogeneousField + click Sample href "../Sample" + + + HomogeneousField <|-- FluorescentHomogeneousThickField + click FluorescentHomogeneousThickField href "../FluorescentHomogeneousThickField" + HomogeneousField <|-- FluorescentHomogeneousThinField + click FluorescentHomogeneousThinField href "../FluorescentHomogeneousThinField" + + + HomogeneousField : description + + HomogeneousField : manufacturer + + HomogeneousField : name + + HomogeneousField : protocol + + + + + HomogeneousField --> "1" Protocol : protocol + click Protocol href "../Protocol" + + + +
    +

    Inheritance

    + +

    Slots

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    NameCardinality and RangeDescriptionInheritance
    protocol1
    Protocol    		The protocol used to prepare the sampleSample
    manufacturer0..1
    String    		The manufacturer of the beadsSample
    name0..1
    String    		The human readable name of an entityNamedObject
    description0..1
    String    		A human readable description of an entityNamedObject
    +

    Usages

    + + + + + + + + + + + + + + + + + +
    used byused intypeused
    FieldIlluminationDatasetsamplerangeHomogeneousField
    +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
      • +
    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfmicroscopemetrics_schema:HomogeneousField
    nativemicroscopemetrics_schema:HomogeneousField
    +

    LinkML Source

    + +

    Direct

    +
    +
    name: HomogeneousField
+description: An homogeneous field.
+from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+is_a: Sample
+abstract: true
+
+
    +
    +

    Induced

    +
    +
    name: HomogeneousField
+description: An homogeneous field.
+from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+is_a: Sample
+abstract: true
+attributes:
+  protocol:
+    name: protocol
+    description: The protocol used to prepare the sample
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
+    rank: 1000
+    alias: protocol
+    owner: HomogeneousField
+    domain_of:
+    - Sample
+    range: Protocol
+    required: true
+    multivalued: false
+    inlined: false
+  manufacturer:
+    name: manufacturer
+    description: The manufacturer of the beads.
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
+    alias: manufacturer
+    owner: HomogeneousField
+    domain_of:
+    - Microscope
+    - Sample
+    range: string
+    required: false
+  name:
+    name: name
+    description: The human readable name of an entity
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+    rank: 1000
+    alias: name
+    owner: HomogeneousField
+    domain_of:
+    - NamedObject
+    - Experimenter
+    range: string
+    required: false
+    multivalued: false
+  description:
+    name: description
+    description: A human readable description of an entity
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+    rank: 1000
+    alias: description
+    owner: HomogeneousField
+    domain_of:
+    - NamedObject
+    - Tag
+    range: string
+    required: false
+    multivalued: false
+
+
    +
    +
    +
    + +
    +
    + +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/Image/index.html b/Image/index.html index dceee1b7..9177d6cc 100644 --- a/Image/index.html +++ b/Image/index.html @@ -7,7 +7,7 @@ - + Class: Image - microscopemetrics-schema @@ -209,31 +209,54 @@

    Class: Image

    URI: microscopemetrics_schema:Image

    classDiagram class Image + click Image href "../Image" MetricsObject <|-- Image + click MetricsObject href "../MetricsObject" Image <|-- ImageMask + click ImageMask href "../ImageMask" Image : acquisition_datetime Image : array_data - Image --> MetaObject : array_data + + + + Image --> "0..1" MetaObject : array_data + click MetaObject href "../MetaObject" + Image : channel_series - Image --> ChannelSeries : channel_series + + + + Image --> "0..1" ChannelSeries : channel_series + click ChannelSeries href "../ChannelSeries" + Image : data_reference - Image --> DataReference : data_reference + + + + Image --> "0..1" DataReference : data_reference + click DataReference href "../DataReference" + Image : description Image : linked_references - Image --> DataReference : linked_references + + + + Image --> "*" DataReference : linked_references + click DataReference href "../DataReference" + Image : name @@ -249,11 +272,21 @@

    Class: Image

    Image : source_images - Image --> DataReference : source_images + + + + Image --> "*" DataReference : source_images + click DataReference href "../DataReference" + Image : time_series - Image --> TimeSeries : time_series + + + + Image --> "0..1" TimeSeries : time_series + click TimeSeries href "../TimeSeries" + Image : voxel_size_x_micron @@ -307,55 +340,55 @@

    Slots

    shape_x -1..1
    Integer +1
    Integer The shape of the image in the x dimension direct shape_y -1..1
    Integer +1
    Integer The shape of the image in the y dimension direct shape_z -1..1
    Integer +1
    Integer The shape of the image in the z dimension direct shape_c -1..1
    Integer +1
    Integer The shape of the image in the c dimension direct shape_t -1..1
    Integer +1
    Integer The shape of the image in the t dimension direct time_series 0..1
    TimeSeries - +A series representing time for time-lapse images direct channel_series 0..1
    ChannelSeries - +A series representing channels for multi-channel images direct acquisition_datetime -1..1
    datetime +0..1
    datetime The datetime of the acquisition direct source_images -0..*
    DataReference +*
    DataReference A list of references linking to the images that were used as a source direct @@ -373,7 +406,7 @@

    Slots

    linked_references -0..*
    DataReference +*
    DataReference A list of linked references MetricsObject @@ -403,26 +436,20 @@

    Usages

    -FieldIlluminationInput +FieldIlluminationInputData field_illumination_image range Image -PSFBeadsInput +PSFBeadsInputData psf_beads_images range Image -ArgolightBInput -argolight_b_image -range -Image - - -ArgolightEInput -argolight_e_image +PSFBeadsOutput +average_bead range Image @@ -466,88 +493,89 @@

    Direct

    description: The physical size in the voxel in the x dimension in microns from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - Image range: float required: false + multivalued: false voxel_size_y_micron: name: voxel_size_y_micron description: The physical size in the voxel in the y dimension in microns from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - Image range: float required: false + multivalued: false voxel_size_z_micron: name: voxel_size_z_micron description: The physical size in the voxel in the z dimension in microns from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - Image range: float required: false + multivalued: false shape_x: name: shape_x description: The shape of the image in the x dimension from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - Image range: integer required: true + multivalued: false shape_y: name: shape_y description: The shape of the image in the y dimension from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - Image range: integer required: true + multivalued: false shape_z: name: shape_z description: The shape of the image in the z dimension from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: int(1) domain_of: - Image range: integer required: true + multivalued: false shape_c: name: shape_c description: The shape of the image in the c dimension from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: int(1) domain_of: - Image range: integer required: true + multivalued: false shape_t: name: shape_t description: The shape of the image in the t dimension from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: int(1) domain_of: - Image range: integer required: true + multivalued: false time_series: name: time_series implements: - linkml:axis0 + description: A series representing time for time-lapse images. from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 domain_of: @@ -558,6 +586,7 @@

    Direct

    name: channel_series implements: - linkml:axis4 + description: A series representing channels for multi-channel images. from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 domain_of: @@ -568,22 +597,22 @@

    Direct

    name: acquisition_datetime description: The datetime of the acquisition from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - multivalued: false domain_of: - MetricsDataset - Image range: datetime - required: true + required: false + multivalued: false source_images: name: source_images description: A list of references linking to the images that were used as a source from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true domain_of: - Image range: DataReference required: false + multivalued: true inlined: true inlined_as_list: true array_data: @@ -591,11 +620,11 @@

    Direct

    description: A non-required slot for non-serializable array data object from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - Image range: MetaObject required: false + multivalued: false @@ -611,67 +640,66 @@

    Induced

    description: The physical size in the voxel in the x dimension in microns from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: voxel_size_x_micron owner: Image domain_of: - Image range: float required: false + multivalued: false voxel_size_y_micron: name: voxel_size_y_micron description: The physical size in the voxel in the y dimension in microns from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: voxel_size_y_micron owner: Image domain_of: - Image range: float required: false + multivalued: false voxel_size_z_micron: name: voxel_size_z_micron description: The physical size in the voxel in the z dimension in microns from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: voxel_size_z_micron owner: Image domain_of: - Image range: float required: false + multivalued: false shape_x: name: shape_x description: The shape of the image in the x dimension from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: shape_x owner: Image domain_of: - Image range: integer required: true + multivalued: false shape_y: name: shape_y description: The shape of the image in the y dimension from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: shape_y owner: Image domain_of: - Image range: integer required: true + multivalued: false shape_z: name: shape_z description: The shape of the image in the z dimension from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: int(1) alias: shape_z owner: Image @@ -679,12 +707,12 @@

    Induced

    - Image range: integer required: true + multivalued: false shape_c: name: shape_c description: The shape of the image in the c dimension from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: int(1) alias: shape_c owner: Image @@ -692,12 +720,12 @@

    Induced

    - Image range: integer required: true + multivalued: false shape_t: name: shape_t description: The shape of the image in the t dimension from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: int(1) alias: shape_t owner: Image @@ -705,10 +733,12 @@

    Induced

    - Image range: integer required: true + multivalued: false time_series: name: time_series implements: - linkml:axis0 + description: A series representing time for time-lapse images. from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 alias: time_series @@ -721,6 +751,7 @@

    Induced

    name: channel_series implements: - linkml:axis4 + description: A series representing channels for multi-channel images. from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 alias: channel_series @@ -733,26 +764,26 @@

    Induced

    name: acquisition_datetime description: The datetime of the acquisition from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - multivalued: false alias: acquisition_datetime owner: Image domain_of: - MetricsDataset - Image range: datetime - required: true + required: false + multivalued: false source_images: name: source_images description: A list of references linking to the images that were used as a source from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: source_images owner: Image domain_of: - Image range: DataReference required: false + multivalued: true inlined: true inlined_as_list: true array_data: @@ -760,37 +791,37 @@

    Induced

    description: A non-required slot for non-serializable array data object from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: array_data owner: Image domain_of: - Image range: MetaObject required: false + multivalued: false data_reference: name: data_reference description: A reference to the data from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: data_reference owner: Image domain_of: - MetricsObject range: DataReference required: false + multivalued: false linked_references: name: linked_references description: A list of linked references from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: linked_references owner: Image domain_of: - MetricsObject range: DataReference required: false + multivalued: true inlined: true inlined_as_list: true name: @@ -798,7 +829,6 @@

    Induced

    description: The human readable name of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: name owner: Image domain_of: @@ -806,12 +836,12 @@

    Induced

    - Experimenter range: string required: false + multivalued: false description: name: description description: A human readable description of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: description owner: Image domain_of: @@ -819,6 +849,7 @@

    Induced

    - Tag range: string required: false + multivalued: false @@ -847,5 +878,7 @@

    Induced

    - + \ No newline at end of file diff --git a/ImageMask/index.html b/ImageMask/index.html index 75a55c54..f39eb2b7 100644 --- a/ImageMask/index.html +++ b/ImageMask/index.html @@ -7,7 +7,7 @@ - + Class: ImageMask - microscopemetrics-schema @@ -209,27 +209,49 @@

    Class: ImageMask

    URI: microscopemetrics_schema:ImageMask

    classDiagram class ImageMask + click ImageMask href "../ImageMask" Image <|-- ImageMask + click Image href "../Image" ImageMask : acquisition_datetime ImageMask : array_data - ImageMask --> MetaObject : array_data + + + + ImageMask --> "0..1" MetaObject : array_data + click MetaObject href "../MetaObject" + ImageMask : channel_series - ImageMask --> ChannelSeries : channel_series + + + + ImageMask --> "0..1" ChannelSeries : channel_series + click ChannelSeries href "../ChannelSeries" + ImageMask : data_reference - ImageMask --> DataReference : data_reference + + + + ImageMask --> "0..1" DataReference : data_reference + click DataReference href "../DataReference" + ImageMask : description ImageMask : linked_references - ImageMask --> DataReference : linked_references + + + + ImageMask --> "*" DataReference : linked_references + click DataReference href "../DataReference" + ImageMask : name @@ -245,11 +267,21 @@

    Class: ImageMask

    ImageMask : source_images - ImageMask --> DataReference : source_images + + + + ImageMask --> "*" DataReference : source_images + click DataReference href "../DataReference" + ImageMask : time_series - ImageMask --> TimeSeries : time_series + + + + ImageMask --> "0..1" TimeSeries : time_series + click TimeSeries href "../TimeSeries" + ImageMask : voxel_size_x_micron @@ -303,55 +335,55 @@

    Slots

    shape_x -1..1
    Integer +1
    Integer The shape of the image in the x dimension Image shape_y -1..1
    Integer +1
    Integer The shape of the image in the y dimension Image shape_z -1..1
    Integer +1
    Integer The shape of the image in the z dimension Image shape_c -1..1
    Integer +1
    Integer The shape of the image in the c dimension Image shape_t -1..1
    Integer +1
    Integer The shape of the image in the t dimension Image time_series 0..1
    TimeSeries - +A series representing time for time-lapse images Image channel_series 0..1
    ChannelSeries - +A series representing channels for multi-channel images Image acquisition_datetime -1..1
    datetime +0..1
    datetime The datetime of the acquisition Image source_images -0..*
    DataReference +*
    DataReference A list of references linking to the images that were used as a source Image @@ -369,7 +401,7 @@

    Slots

    linked_references -0..*
    DataReference +*
    DataReference A list of linked references MetricsObject @@ -404,12 +436,6 @@

    Usages

    range ImageMask - -ArgolightBOutput -spots_labels_image -range -ImageMask -

    Identifier and Mapping Information

    @@ -459,67 +485,66 @@

    Induced

    description: The physical size in the voxel in the x dimension in microns from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: voxel_size_x_micron owner: ImageMask domain_of: - Image range: float required: false + multivalued: false voxel_size_y_micron: name: voxel_size_y_micron description: The physical size in the voxel in the y dimension in microns from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: voxel_size_y_micron owner: ImageMask domain_of: - Image range: float required: false + multivalued: false voxel_size_z_micron: name: voxel_size_z_micron description: The physical size in the voxel in the z dimension in microns from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: voxel_size_z_micron owner: ImageMask domain_of: - Image range: float required: false + multivalued: false shape_x: name: shape_x description: The shape of the image in the x dimension from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: shape_x owner: ImageMask domain_of: - Image range: integer required: true + multivalued: false shape_y: name: shape_y description: The shape of the image in the y dimension from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: shape_y owner: ImageMask domain_of: - Image range: integer required: true + multivalued: false shape_z: name: shape_z description: The shape of the image in the z dimension from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: int(1) alias: shape_z owner: ImageMask @@ -527,12 +552,12 @@

    Induced

    - Image range: integer required: true + multivalued: false shape_c: name: shape_c description: The shape of the image in the c dimension from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: int(1) alias: shape_c owner: ImageMask @@ -540,12 +565,12 @@

    Induced

    - Image range: integer required: true + multivalued: false shape_t: name: shape_t description: The shape of the image in the t dimension from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: int(1) alias: shape_t owner: ImageMask @@ -553,10 +578,12 @@

    Induced

    - Image range: integer required: true + multivalued: false time_series: name: time_series implements: - linkml:axis0 + description: A series representing time for time-lapse images. from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 alias: time_series @@ -569,6 +596,7 @@

    Induced

    name: channel_series implements: - linkml:axis4 + description: A series representing channels for multi-channel images. from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 alias: channel_series @@ -581,26 +609,26 @@

    Induced

    name: acquisition_datetime description: The datetime of the acquisition from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - multivalued: false alias: acquisition_datetime owner: ImageMask domain_of: - MetricsDataset - Image range: datetime - required: true + required: false + multivalued: false source_images: name: source_images description: A list of references linking to the images that were used as a source from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: source_images owner: ImageMask domain_of: - Image range: DataReference required: false + multivalued: true inlined: true inlined_as_list: true array_data: @@ -608,37 +636,37 @@

    Induced

    description: A non-required slot for non-serializable array data object from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: array_data owner: ImageMask domain_of: - Image range: MetaObject required: false + multivalued: false data_reference: name: data_reference description: A reference to the data from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: data_reference owner: ImageMask domain_of: - MetricsObject range: DataReference required: false + multivalued: false linked_references: name: linked_references description: A list of linked references from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: linked_references owner: ImageMask domain_of: - MetricsObject range: DataReference required: false + multivalued: true inlined: true inlined_as_list: true name: @@ -646,7 +674,6 @@

    Induced

    description: The human readable name of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: name owner: ImageMask domain_of: @@ -654,12 +681,12 @@

    Induced

    - Experimenter range: string required: false + multivalued: false description: name: description description: A human readable description of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: description owner: ImageMask domain_of: @@ -667,6 +694,7 @@

    Induced

    - Tag range: string required: false + multivalued: false @@ -695,5 +723,7 @@

    Induced

    - + \ No newline at end of file diff --git a/Integer/index.html b/Integer/index.html index 257f8ad9..dcb53a62 100644 --- a/Integer/index.html +++ b/Integer/index.html @@ -11,7 +11,7 @@ - + diff --git a/Jsonpath/index.html b/Jsonpath/index.html index e2b93949..081fb781 100644 --- a/Jsonpath/index.html +++ b/Jsonpath/index.html @@ -11,7 +11,7 @@ - + diff --git a/Jsonpointer/index.html b/Jsonpointer/index.html index e7cb0219..5163774f 100644 --- a/Jsonpointer/index.html +++ b/Jsonpointer/index.html @@ -11,7 +11,7 @@ - + diff --git a/ArgolightBCentersOfMass/index.html b/KeyMeasurements/index.html similarity index 72% rename from ArgolightBCentersOfMass/index.html rename to KeyMeasurements/index.html index dbd21965..7222ce52 100644 --- a/ArgolightBCentersOfMass/index.html +++ b/KeyMeasurements/index.html @@ -5,10 +5,10 @@ - + - -Class: ArgolightBCentersOfMass - microscopemetrics-schema + +Class: KeyMeasurements - microscopemetrics-schema @@ -21,7 +21,7 @@
    - + Skip to content
    @@ -45,7 +45,7 @@
    - Class: ArgolightBCentersOfMass + Class: KeyMeasurements
    @@ -152,11 +152,6 @@
  • - - Usages - -
    • -
  • Identifier and Mapping Information @@ -201,51 +196,58 @@
    - + -

    Class: ArgolightBCentersOfMass

    -

    URI: microscopemetrics_schema:ArgolightBCentersOfMass

    +

    Class: KeyMeasurements

    +

    A table of key measurements

    +
      +
    • NOTE: this is an abstract class and should not be instantiated directly
      • +
    +

    URI: microscopemetrics_schema:KeyMeasurements

    classDiagram - class ArgolightBCentersOfMass - CentersOfMass <|-- ArgolightBCentersOfMass - Roi <|-- ArgolightBCentersOfMass + class KeyMeasurements + click KeyMeasurements href "../KeyMeasurements" + KeyValues <|-- KeyMeasurements + click KeyValues href "../KeyValues" + - ArgolightBCentersOfMass : data_reference + KeyMeasurements <|-- FieldIlluminationKeyMeasurements + click FieldIlluminationKeyMeasurements href "../FieldIlluminationKeyMeasurements" + KeyMeasurements <|-- PSFBeadsKeyMeasurements + click PSFBeadsKeyMeasurements href "../PSFBeadsKeyMeasurements" - ArgolightBCentersOfMass --> DataReference : data_reference - ArgolightBCentersOfMass : description + KeyMeasurements : data_reference - ArgolightBCentersOfMass : ellipses - ArgolightBCentersOfMass --> Ellipse : ellipses - ArgolightBCentersOfMass : lines - ArgolightBCentersOfMass --> Line : lines + KeyMeasurements --> "0..1" DataReference : data_reference + click DataReference href "../DataReference" - ArgolightBCentersOfMass : linked_references - ArgolightBCentersOfMass --> DataReference : linked_references + KeyMeasurements : description - ArgolightBCentersOfMass : masks + KeyMeasurements : linked_references - ArgolightBCentersOfMass --> Mask : masks - ArgolightBCentersOfMass : name - ArgolightBCentersOfMass : points - ArgolightBCentersOfMass --> Point : points + KeyMeasurements --> "*" DataReference : linked_references + click DataReference href "../DataReference" - ArgolightBCentersOfMass : polygons - ArgolightBCentersOfMass --> Polygon : polygons + KeyMeasurements : name - ArgolightBCentersOfMass : rectangles + KeyMeasurements : table_data + + + + + KeyMeasurements --> "0..1" MetaObject : table_data + click MetaObject href "../MetaObject" - ArgolightBCentersOfMass --> Rectangle : rectangles
    @@ -253,8 +255,12 @@

    Inheritance

    • NamedObject
      • MetricsObject
          -
        • Roi @@ -274,40 +280,10 @@

          Slots

          -points -0..*
          Point -A list of points included in the ROI -Roi - - -lines -0..*
          Line -A list of lines included in the ROI -Roi - - -rectangles -0..*
          Rectangle -A list of rectangles included in the ROI -Roi - - -ellipses -0..*
          Ellipse -A list of ellipses included in the ROI -Roi - - -polygons -0..*
          Polygon -A list of polygons included in the ROI -Roi - - -masks -0..*
          Mask -A list of masks included in the ROI -Roi +table_data +0..1
          MetaObject +A non-required slot for non-serializable table data object +direct data_reference @@ -317,7 +293,7 @@

          Slots

          linked_references -0..*
          DataReference +*
          DataReference A list of linked references MetricsObject @@ -335,25 +311,6 @@

          Slots

          -

          Usages

          - - - - - - - - - - - - - - - - - -
          used byused intypeused
          ArgolightBOutputspots_centers_of_massrangeArgolightBCentersOfMass

          Identifier and Mapping Information

          Schema Source

            @@ -370,11 +327,11 @@

            Mappings

            self -microscopemetrics_schema:ArgolightBCentersOfMass +microscopemetrics_schema:KeyMeasurements native -microscopemetrics_schema:ArgolightBCentersOfMass +microscopemetrics_schema:KeyMeasurements @@ -382,130 +339,71 @@

            LinkML Source

            Direct

            -
            name: ArgolightBCentersOfMass
+
            name: KeyMeasurements
+description: A table of key measurements
 from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: Roi
-mixins:
-- CentersOfMass
+is_a: KeyValues
+abstract: true
+attributes:
+  table_data:
+    name: table_data
+    description: A non-required slot for non-serializable table data object
+    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
+    rank: 1000
+    domain_of:
+    - KeyMeasurements
+    - Table
+    range: MetaObject
+    required: false
+    multivalued: false

            Induced

            -
            name: ArgolightBCentersOfMass
+
            name: KeyMeasurements
+description: A table of key measurements
 from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
-is_a: Roi
-mixins:
-- CentersOfMass
+is_a: KeyValues
+abstract: true
 attributes:
-  points:
-    name: points
-    description: A list of points included in the ROI
+  table_data:
+    name: table_data
+    description: A non-required slot for non-serializable table data object
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
     rank: 1000
-    multivalued: true
-    alias: points
-    owner: ArgolightBCentersOfMass
+    alias: table_data
+    owner: KeyMeasurements
     domain_of:
-    - Roi
-    range: Point
+    - KeyMeasurements
+    - Table
+    range: MetaObject
     required: false
-    inlined: true
-    inlined_as_list: true
-  lines:
-    name: lines
-    description: A list of lines included in the ROI
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: lines
-    owner: ArgolightBCentersOfMass
-    domain_of:
-    - Roi
-    range: Line
-    required: false
-    inlined: true
-    inlined_as_list: true
-  rectangles:
-    name: rectangles
-    description: A list of rectangles included in the ROI
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: rectangles
-    owner: ArgolightBCentersOfMass
-    domain_of:
-    - Roi
-    range: Rectangle
-    required: false
-    inlined: true
-    inlined_as_list: true
-  ellipses:
-    name: ellipses
-    description: A list of ellipses included in the ROI
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: ellipses
-    owner: ArgolightBCentersOfMass
-    domain_of:
-    - Roi
-    range: Ellipse
-    required: false
-    inlined: true
-    inlined_as_list: true
-  polygons:
-    name: polygons
-    description: A list of polygons included in the ROI
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: polygons
-    owner: ArgolightBCentersOfMass
-    domain_of:
-    - Roi
-    range: Polygon
-    required: false
-    inlined: true
-    inlined_as_list: true
-  masks:
-    name: masks
-    description: A list of masks included in the ROI
-    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
-    rank: 1000
-    multivalued: true
-    alias: masks
-    owner: ArgolightBCentersOfMass
-    domain_of:
-    - Roi
-    range: Mask
-    required: false
-    inlined: true
-    inlined_as_list: true
+    multivalued: false
   data_reference:
     name: data_reference
     description: A reference to the data
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
     rank: 1000
-    multivalued: false
     alias: data_reference
-    owner: ArgolightBCentersOfMass
+    owner: KeyMeasurements
     domain_of:
     - MetricsObject
     range: DataReference
     required: false
+    multivalued: false
   linked_references:
     name: linked_references
     description: A list of linked references
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema
     rank: 1000
-    multivalued: true
     alias: linked_references
-    owner: ArgolightBCentersOfMass
+    owner: KeyMeasurements
     domain_of:
     - MetricsObject
     range: DataReference
     required: false
+    multivalued: true
     inlined: true
     inlined_as_list: true
   name:
@@ -513,27 +411,27 @@ 
            Induced
            
     description: The human readable name of an entity
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: false
     alias: name
-    owner: ArgolightBCentersOfMass
+    owner: KeyMeasurements
     domain_of:
     - NamedObject
     - Experimenter
     range: string
     required: false
+    multivalued: false
   description:
     name: description
     description: A human readable description of an entity
     from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
     rank: 1000
-    multivalued: false
     alias: description
-    owner: ArgolightBCentersOfMass
+    owner: KeyMeasurements
     domain_of:
     - NamedObject
     - Tag
     range: string
     required: false
+    multivalued: false
            @@ -562,5 +460,7 @@

            Induced

    - + \ No newline at end of file diff --git a/KeyValues/index.html b/KeyValues/index.html index 96c742f7..7df79767 100644 --- a/KeyValues/index.html +++ b/KeyValues/index.html @@ -7,7 +7,7 @@ - + Class: KeyValues - microscopemetrics-schema @@ -207,25 +207,34 @@

    Class: KeyValues

    URI: microscopemetrics_schema:KeyValues

    classDiagram class KeyValues + click KeyValues href "../KeyValues" MetricsObject <|-- KeyValues + click MetricsObject href "../MetricsObject" - KeyValues <|-- FieldIlluminationKeyValues - KeyValues <|-- PSFBeadsKeyValues - KeyValues <|-- ArgolightBIntensityKeyValues - KeyValues <|-- ArgolightBDistanceKeyValues - KeyValues <|-- ArgolightEKeyValues + KeyValues <|-- KeyMeasurements + click KeyMeasurements href "../KeyMeasurements" KeyValues : data_reference - KeyValues --> DataReference : data_reference + + + + KeyValues --> "0..1" DataReference : data_reference + click DataReference href "../DataReference" + KeyValues : description KeyValues : linked_references - KeyValues --> DataReference : linked_references + + + + KeyValues --> "*" DataReference : linked_references + click DataReference href "../DataReference" + KeyValues : name @@ -236,11 +245,7 @@

    Inheritance

  • NamedObject
    • MetricsObject @@ -267,7 +272,7 @@

      Slots

      linked_references -0..*
      DataReference +*
      DataReference A list of linked references MetricsObject @@ -334,25 +339,25 @@

      Induced

      description: A reference to the data from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: data_reference owner: KeyValues domain_of: - MetricsObject range: DataReference required: false + multivalued: false linked_references: name: linked_references description: A list of linked references from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: linked_references owner: KeyValues domain_of: - MetricsObject range: DataReference required: false + multivalued: true inlined: true inlined_as_list: true name: @@ -360,7 +365,6 @@

      Induced

      description: The human readable name of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: name owner: KeyValues domain_of: @@ -368,12 +372,12 @@

      Induced

      - Experimenter range: string required: false + multivalued: false description: name: description description: A human readable description of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: description owner: KeyValues domain_of: @@ -381,6 +385,7 @@

      Induced

      - Tag range: string required: false + multivalued: false       @@ -409,5 +414,7 @@

      Induced

      - + \ No newline at end of file diff --git a/Line/index.html b/Line/index.html index 14685bd5..dbedf35b 100644 --- a/Line/index.html +++ b/Line/index.html @@ -7,7 +7,7 @@ - + Class: Line - microscopemetrics-schema @@ -209,7 +209,9 @@

      Class: Line

      URI: microscopemetrics_schema:Line

      classDiagram class Line + click Line href "../Line" Shape <|-- Line + click Shape href "../Shape" Line : c @@ -217,13 +219,23 @@

      Class: Line

      Line : fill_color - Line --> Color : fill_color + + + + Line --> "0..1" Color : fill_color + click Color href "../Color" + Line : name Line : stroke_color - Line --> Color : stroke_color + + + + Line --> "0..1" Color : stroke_color + click Color href "../Color" + Line : stroke_width @@ -264,25 +276,25 @@

      Slots

      x1 -1..1
      Float +1
      Float The x coordinate of the first point of the line direct y1 -1..1
      Float +1
      Float The y coordinate of the first point of the line direct x2 -1..1
      Float +1
      Float The x coordinate of the second point of the line direct y2 -1..1
      Float +1
      Float The y coordinate of the second point of the line direct @@ -353,12 +365,6 @@

      Usages

      range Line - -ArgolightBCentersOfMass -lines -range -Line -

      Identifier and Mapping Information

      @@ -399,41 +405,41 @@

      Direct

      description: The x coordinate of the first point of the line from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - Line range: float required: true + multivalued: false y1: name: y1 description: The y coordinate of the first point of the line from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - Line range: float required: true + multivalued: false x2: name: x2 description: The x coordinate of the second point of the line from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - Line range: float required: true + multivalued: false y2: name: y2 description: The y coordinate of the second point of the line from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - Line range: float required: true + multivalued: false       @@ -449,49 +455,49 @@

      Induced

      description: The x coordinate of the first point of the line from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: x1 owner: Line domain_of: - Line range: float required: true + multivalued: false y1: name: y1 description: The y coordinate of the first point of the line from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: y1 owner: Line domain_of: - Line range: float required: true + multivalued: false x2: name: x2 description: The x coordinate of the second point of the line from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: x2 owner: Line domain_of: - Line range: float required: true + multivalued: false y2: name: y2 description: The y coordinate of the second point of the line from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: y2 owner: Line domain_of: - Line range: float required: true + multivalued: false z: name: z description: The z coordinate of the shape @@ -564,7 +570,6 @@

      Induced

      description: The human readable name of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: name owner: Line domain_of: @@ -572,12 +577,12 @@

      Induced

      - Experimenter range: string required: false + multivalued: false description: name: description description: A human readable description of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: description owner: Line domain_of: @@ -585,6 +590,7 @@

      Induced

      - Tag range: string required: false + multivalued: false @@ -613,5 +619,7 @@

      Induced

      - + \ No newline at end of file diff --git a/Mask/index.html b/Mask/index.html index dc3d75c1..72ba45a7 100644 --- a/Mask/index.html +++ b/Mask/index.html @@ -7,7 +7,7 @@ - + Class: Mask - microscopemetrics-schema @@ -209,7 +209,9 @@

      Class: Mask

      URI: microscopemetrics_schema:Mask

      classDiagram class Mask + click Mask href "../Mask" Shape <|-- Mask + click Shape href "../Shape" Mask : c @@ -217,17 +219,32 @@

      Class: Mask

      Mask : fill_color - Mask --> Color : fill_color + + + + Mask --> "0..1" Color : fill_color + click Color href "../Color" + Mask : mask - Mask --> ImageMask : mask + + + + Mask --> "0..1" ImageMask : mask + click ImageMask href "../ImageMask" + Mask : name Mask : stroke_color - Mask --> Color : stroke_color + + + + Mask --> "0..1" Color : stroke_color + click Color href "../Color" + Mask : stroke_width @@ -264,13 +281,13 @@

      Slots

      y -1..1
      Integer +1
      Integer The y coordinate of the top left corner of the mask direct x -1..1
      Integer +1
      Integer The x coordinate of the top left corner of the mask direct @@ -347,12 +364,6 @@

      Usages

      range Mask - -ArgolightBCentersOfMass -masks -range -Mask -

      Identifier and Mapping Information

      @@ -419,10 +430,10 @@

      Direct

      description: The mask image from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - Mask range: ImageMask + multivalued: false @@ -468,12 +479,12 @@

      Induced

      description: The mask image from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: mask owner: Mask domain_of: - Mask range: ImageMask + multivalued: false z: name: z description: The z coordinate of the shape @@ -546,7 +557,6 @@

      Induced

      description: The human readable name of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: name owner: Mask domain_of: @@ -554,12 +564,12 @@

      Induced

      - Experimenter range: string required: false + multivalued: false description: name: description description: A human readable description of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: description owner: Mask domain_of: @@ -567,6 +577,7 @@

      Induced

      - Tag range: string required: false + multivalued: false @@ -595,5 +606,7 @@

      Induced

      - + \ No newline at end of file diff --git a/MetaObject/index.html b/MetaObject/index.html index 4b194602..d54845c8 100644 --- a/MetaObject/index.html +++ b/MetaObject/index.html @@ -7,7 +7,7 @@ - + Class: MetaObject - microscopemetrics-schema @@ -203,6 +203,7 @@

      Class: MetaObject

      URI: linkml:Any

      classDiagram class MetaObject + click MetaObject href "../MetaObject"
      @@ -249,11 +250,29 @@

      Usages

      MetaObject +KeyMeasurements +table_data +range +MetaObject + + Table table_data range MetaObject + +FieldIlluminationKeyMeasurements +table_data +range +MetaObject + + +PSFBeadsKeyMeasurements +table_data +range +MetaObject +

      Identifier and Mapping Information

      @@ -323,5 +342,7 @@

      Induced

      - + \ No newline at end of file diff --git a/MetricsDataset/index.html b/MetricsDataset/index.html index 043be88a..f705cb78 100644 --- a/MetricsDataset/index.html +++ b/MetricsDataset/index.html @@ -7,7 +7,7 @@ - + Class: MetricsDataset - microscopemetrics-schema @@ -206,53 +206,102 @@

      Class: MetricsDataset

      A base object on which microscope-metrics runs the analysis

      +
        +
      • NOTE: this is an abstract class and should not be instantiated directly
        • +

      URI: microscopemetrics_schema:MetricsDataset

      classDiagram class MetricsDataset + click MetricsDataset href "../MetricsDataset" MetricsObject <|-- MetricsDataset + click MetricsObject href "../MetricsObject" MetricsDataset <|-- FieldIlluminationDataset + click FieldIlluminationDataset href "../FieldIlluminationDataset" MetricsDataset <|-- PSFBeadsDataset - MetricsDataset <|-- ArgolightBDataset - MetricsDataset <|-- ArgolightEDataset + click PSFBeadsDataset href "../PSFBeadsDataset" MetricsDataset : acquisition_datetime MetricsDataset : data_reference - MetricsDataset --> DataReference : data_reference + + + + MetricsDataset --> "0..1" DataReference : data_reference + click DataReference href "../DataReference" + MetricsDataset : description MetricsDataset : experimenter - MetricsDataset --> Experimenter : experimenter - MetricsDataset : input - MetricsDataset --> MetricsInput : input + + MetricsDataset --> "0..1" Experimenter : experimenter + click Experimenter href "../Experimenter" + + + MetricsDataset : input_data + + + + + MetricsDataset --> "1" MetricsInputData : input_data + click MetricsInputData href "../MetricsInputData" + + + MetricsDataset : input_parameters + + + + + MetricsDataset --> "1" MetricsInputParameters : input_parameters + click MetricsInputParameters href "../MetricsInputParameters" + MetricsDataset : linked_references - MetricsDataset --> DataReference : linked_references + + + + MetricsDataset --> "*" DataReference : linked_references + click DataReference href "../DataReference" + MetricsDataset : microscope - MetricsDataset --> Microscope : microscope + + + + MetricsDataset --> "1" Microscope : microscope + click Microscope href "../Microscope" + MetricsDataset : name MetricsDataset : output - MetricsDataset --> MetricsOutput : output + + + + MetricsDataset --> "0..1" MetricsOutput : output + click MetricsOutput href "../MetricsOutput" + MetricsDataset : processed MetricsDataset : sample - MetricsDataset --> Sample : sample + + + + MetricsDataset --> "0..1" Sample : sample + click Sample href "../Sample" +
      @@ -263,8 +312,6 @@

      Inheritance

    • MetricsDataset
    @@ -284,15 +331,15 @@

    Slots

    -microscope -1..1
    Microscope -The microscope that was used to acquire the dataset +sample +0..1
    Sample +The physical sample that was imaged direct -sample -0..1
    Sample -The sample that was imaged +microscope +1
    Microscope +The microscope that was used to acquire the dataset direct @@ -309,14 +356,20 @@

    Slots

    processed -1..1
    Boolean +1
    Boolean Has the dataset been processed by microscope-metrics direct -input -1..1
    MetricsInput -The input of the analysis +input_data +1
    MetricsInputData +The input data for the analysis +direct + + +input_parameters +1
    MetricsInputParameters +The input parameters for the analysis direct @@ -333,7 +386,7 @@

    Slots

    linked_references -0..*
    DataReference +*
    DataReference A list of linked references MetricsObject @@ -408,84 +461,80 @@

    Direct

    description: A base object on which microscope-metrics runs the analysis from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema is_a: MetricsObject +abstract: true +slots: +- sample attributes: microscope: name: microscope description: The microscope that was used to acquire the dataset from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 - multivalued: false domain_of: - MetricsDataset range: Microscope required: true - sample: - name: sample - description: The sample that was imaged - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 multivalued: false - domain_of: - - MetricsDataset - range: Sample experimenter: name: experimenter description: The experimenter that performed the imaging experiment from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 - multivalued: false domain_of: - MetricsDataset range: Experimenter + multivalued: false acquisition_datetime: name: acquisition_datetime description: The datetime of the acquisition from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 - multivalued: false domain_of: - MetricsDataset - Image range: datetime + multivalued: false processed: name: processed description: Has the dataset been processed by microscope-metrics from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: 'False' domain_of: - MetricsDataset range: boolean required: true - input: - name: input - description: The input of the analysis + multivalued: false + input_data: + name: input_data + description: The input data for the analysis from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 + domain_of: + - MetricsDataset + - FieldIlluminationDataset + - PSFBeadsDataset + range: MetricsInputData + required: true multivalued: false + input_parameters: + name: input_parameters + description: The input parameters for the analysis + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema domain_of: - MetricsDataset - FieldIlluminationDataset - PSFBeadsDataset - - ArgolightBDataset - - ArgolightEDataset - range: MetricsInput + range: MetricsInputParameters required: true + multivalued: false output: name: output description: The output of the analysis from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 - multivalued: false domain_of: - MetricsDataset - FieldIlluminationDataset - PSFBeadsDataset - - ArgolightBDataset - - ArgolightEDataset range: MetricsOutput required: false + multivalued: false tree_root: true rules: - preconditions: @@ -507,59 +556,45 @@

    Induced

    description: A base object on which microscope-metrics runs the analysis from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema is_a: MetricsObject +abstract: true attributes: microscope: name: microscope description: The microscope that was used to acquire the dataset from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 - multivalued: false alias: microscope owner: MetricsDataset domain_of: - MetricsDataset range: Microscope required: true - sample: - name: sample - description: The sample that was imaged - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 multivalued: false - alias: sample - owner: MetricsDataset - domain_of: - - MetricsDataset - range: Sample experimenter: name: experimenter description: The experimenter that performed the imaging experiment from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 - multivalued: false alias: experimenter owner: MetricsDataset domain_of: - MetricsDataset range: Experimenter + multivalued: false acquisition_datetime: name: acquisition_datetime description: The datetime of the acquisition from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 - multivalued: false alias: acquisition_datetime owner: MetricsDataset domain_of: - MetricsDataset - Image range: datetime + multivalued: false processed: name: processed description: Has the dataset been processed by microscope-metrics from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: 'False' alias: processed owner: MetricsDataset @@ -567,62 +602,84 @@

    Induced

    - MetricsDataset range: boolean required: true - input: - name: input - description: The input of the analysis + multivalued: false + input_data: + name: input_data + description: The input data for the analysis from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 + alias: input_data + owner: MetricsDataset + domain_of: + - MetricsDataset + - FieldIlluminationDataset + - PSFBeadsDataset + range: MetricsInputData + required: true multivalued: false - alias: input + input_parameters: + name: input_parameters + description: The input parameters for the analysis + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema + alias: input_parameters owner: MetricsDataset domain_of: - MetricsDataset - FieldIlluminationDataset - PSFBeadsDataset - - ArgolightBDataset - - ArgolightEDataset - range: MetricsInput + range: MetricsInputParameters required: true + multivalued: false output: name: output description: The output of the analysis from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 - multivalued: false alias: output owner: MetricsDataset domain_of: - MetricsDataset - FieldIlluminationDataset - PSFBeadsDataset - - ArgolightBDataset - - ArgolightEDataset range: MetricsOutput required: false + multivalued: false + sample: + name: sample + description: The physical sample that was imaged + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema + rank: 1000 + alias: sample + owner: MetricsDataset + domain_of: + - MetricsDataset + - FieldIlluminationDataset + - PSFBeadsDataset + range: Sample + required: false + multivalued: false data_reference: name: data_reference description: A reference to the data from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: data_reference owner: MetricsDataset domain_of: - MetricsObject range: DataReference required: false + multivalued: false linked_references: name: linked_references description: A list of linked references from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: linked_references owner: MetricsDataset domain_of: - MetricsObject range: DataReference required: false + multivalued: true inlined: true inlined_as_list: true name: @@ -630,7 +687,6 @@

    Induced

    description: The human readable name of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: name owner: MetricsDataset domain_of: @@ -638,12 +694,12 @@

    Induced

    - Experimenter range: string required: false + multivalued: false description: name: description description: A human readable description of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: description owner: MetricsDataset domain_of: @@ -651,6 +707,7 @@

    Induced

    - Tag range: string required: false + multivalued: false tree_root: true rules: - preconditions: @@ -691,5 +748,7 @@

    Induced

    - + \ No newline at end of file diff --git a/MetricsDatasetCollection/index.html b/MetricsDatasetCollection/index.html index 07210bf8..ae7d18ac 100644 --- a/MetricsDatasetCollection/index.html +++ b/MetricsDatasetCollection/index.html @@ -7,7 +7,7 @@ - + Class: MetricsDatasetCollection - microscopemetrics-schema @@ -204,25 +204,43 @@

    Class: MetricsDatasetCollection

    URI: microscopemetrics_schema:MetricsDatasetCollection

    classDiagram class MetricsDatasetCollection + click MetricsDatasetCollection href "../MetricsDatasetCollection" MetricsObject <|-- MetricsDatasetCollection + click MetricsObject href "../MetricsObject" MetricsDatasetCollection <|-- HarmonizedMetricsDatasetCollection + click HarmonizedMetricsDatasetCollection href "../HarmonizedMetricsDatasetCollection" MetricsDatasetCollection : data_reference - MetricsDatasetCollection --> DataReference : data_reference + + + + MetricsDatasetCollection --> "0..1" DataReference : data_reference + click DataReference href "../DataReference" + MetricsDatasetCollection : datasets - MetricsDatasetCollection --> MetricsDataset : datasets + + + + MetricsDatasetCollection --> "*" MetricsDataset : datasets + click MetricsDataset href "../MetricsDataset" + MetricsDatasetCollection : description MetricsDatasetCollection : linked_references - MetricsDatasetCollection --> DataReference : linked_references + + + + MetricsDatasetCollection --> "*" DataReference : linked_references + click DataReference href "../DataReference" + MetricsDatasetCollection : name @@ -254,7 +272,7 @@

    Slots

    datasets -0..*
    MetricsDataset +*
    MetricsDataset The datasets of the collection direct @@ -266,7 +284,7 @@

    Slots

    linked_references -0..*
    DataReference +*
    DataReference A list of linked references MetricsObject @@ -322,10 +340,10 @@

    Direct

    description: The datasets of the collection from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true domain_of: - MetricsDatasetCollection range: MetricsDataset + multivalued: true inlined: true inlined_as_list: true @@ -343,12 +361,12 @@

    Induced

    description: The datasets of the collection from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: datasets owner: MetricsDatasetCollection domain_of: - MetricsDatasetCollection range: MetricsDataset + multivalued: true inlined: true inlined_as_list: true data_reference: @@ -356,25 +374,25 @@

    Induced

    description: A reference to the data from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: data_reference owner: MetricsDatasetCollection domain_of: - MetricsObject range: DataReference required: false + multivalued: false linked_references: name: linked_references description: A list of linked references from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: linked_references owner: MetricsDatasetCollection domain_of: - MetricsObject range: DataReference required: false + multivalued: true inlined: true inlined_as_list: true name: @@ -382,7 +400,6 @@

    Induced

    description: The human readable name of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: name owner: MetricsDatasetCollection domain_of: @@ -390,12 +407,12 @@

    Induced

    - Experimenter range: string required: false + multivalued: false description: name: description description: A human readable description of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: description owner: MetricsDatasetCollection domain_of: @@ -403,6 +420,7 @@

    Induced

    - Tag range: string required: false + multivalued: false @@ -431,5 +449,7 @@

    Induced

    - + \ No newline at end of file diff --git a/MetricsInput/index.html b/MetricsInputData/index.html similarity index 88% rename from MetricsInput/index.html rename to MetricsInputData/index.html index f47e11f0..29155db4 100644 --- a/MetricsInput/index.html +++ b/MetricsInputData/index.html @@ -5,10 +5,10 @@ - + - -Class: MetricsInput - microscopemetrics-schema + +Class: MetricsInputData - microscopemetrics-schema @@ -21,7 +21,7 @@
    - + Skip to content
    @@ -45,7 +45,7 @@
    - Class: MetricsInput + Class: MetricsInputData
    @@ -201,31 +201,30 @@
    - + -

    Class: MetricsInput

    -

    An abstract class for analysis inputs

    +

    Class: MetricsInputData

    +

    An abstract class for analysis input data

    • NOTE: this is an abstract class and should not be instantiated directly
    -

    URI: microscopemetrics_schema:MetricsInput

    +

    URI: microscopemetrics_schema:MetricsInputData

    classDiagram - class MetricsInput - MetricsInput <|-- FieldIlluminationInput - MetricsInput <|-- PSFBeadsInput - MetricsInput <|-- ArgolightBInput - MetricsInput <|-- ArgolightEInput + class MetricsInputData + click MetricsInputData href "../MetricsInputData" + MetricsInputData <|-- FieldIlluminationInputData + click FieldIlluminationInputData href "../FieldIlluminationInputData" + MetricsInputData <|-- PSFBeadsInputData + click PSFBeadsInputData href "../PSFBeadsInputData"

    Inheritance

      -
    • MetricsInput @@ -261,9 +260,9 @@

      Usages

      MetricsDataset -input +input_data range -MetricsInput +MetricsInputData @@ -283,11 +282,11 @@

      Mappings

      self -microscopemetrics_schema:MetricsInput +microscopemetrics_schema:MetricsInputData native -microscopemetrics_schema:MetricsInput +microscopemetrics_schema:MetricsInputData @@ -295,8 +294,8 @@

      LinkML Source

      Direct

      -
      name: MetricsInput
-description: An abstract class for analysis inputs
+
      name: MetricsInputData
+description: An abstract class for analysis input data
 from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
 abstract: true
 
@@ -304,8 +303,8 @@ 
      Direct

      Induced

      -
      name: MetricsInput
-description: An abstract class for analysis inputs
+
      name: MetricsInputData
+description: An abstract class for analysis input data
 from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
 abstract: true
 
@@ -336,5 +335,7 @@ 
      Induced
    - + \ No newline at end of file diff --git a/MetricsInputParameters/index.html b/MetricsInputParameters/index.html new file mode 100644 index 00000000..3a4c21cc --- /dev/null +++ b/MetricsInputParameters/index.html @@ -0,0 +1,341 @@ + + + + + + + + + + +Class: MetricsInputParameters - microscopemetrics-schema + + + + + + + + + + + + +
    +
    +
    + +
    +
    +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    +
    + +
    +
    +
    +
    +
    + + + +

    Class: MetricsInputParameters

    +

    An abstract class for analysis inputs parameters

    +
      +
    • NOTE: this is an abstract class and should not be instantiated directly
      • +
    +

    URI: microscopemetrics_schema:MetricsInputParameters

    +
    classDiagram + class MetricsInputParameters + click MetricsInputParameters href "../MetricsInputParameters" + MetricsInputParameters <|-- FieldIlluminationInputParameters + click FieldIlluminationInputParameters href "../FieldIlluminationInputParameters" + MetricsInputParameters <|-- PSFBeadsInputParameters + click PSFBeadsInputParameters href "../PSFBeadsInputParameters" + + +
    +

    Inheritance

    + +

    Slots

    + + + + + + + + + + + + + + + + + +
    NameCardinality and RangeDescriptionInheritance
    +

    Usages

    + + + + + + + + + + + + + + + + + +
    used byused intypeused
    MetricsDatasetinput_parametersrangeMetricsInputParameters
    +

    Identifier and Mapping Information

    +

    Schema Source

    +
      +
    • from schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
      • +
    +

    Mappings

    + + + + + + + + + + + + + + + + + +
    Mapping TypeMapped Value
    selfmicroscopemetrics_schema:MetricsInputParameters
    nativemicroscopemetrics_schema:MetricsInputParameters
    +

    LinkML Source

    + +

    Direct

    +
    +
    name: MetricsInputParameters
+description: An abstract class for analysis inputs parameters
+from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+abstract: true
+
+
    +
    +

    Induced

    +
    +
    name: MetricsInputParameters
+description: An abstract class for analysis inputs parameters
+from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema
+abstract: true
+
+
    +
    +
    +
    + +
    +
    + +
    +
    +
    +
    + + + + \ No newline at end of file diff --git a/MetricsObject/index.html b/MetricsObject/index.html index 11d4b451..4b15e6f9 100644 --- a/MetricsObject/index.html +++ b/MetricsObject/index.html @@ -7,7 +7,7 @@ - + Class: MetricsObject - microscopemetrics-schema @@ -207,28 +207,50 @@

    Class: MetricsObject

    URI: microscopemetrics_schema:MetricsObject

    classDiagram class MetricsObject + click MetricsObject href "../MetricsObject" NamedObject <|-- MetricsObject + click NamedObject href "../NamedObject" MetricsObject <|-- Microscope + click Microscope href "../Microscope" MetricsObject <|-- MetricsDatasetCollection + click MetricsDatasetCollection href "../MetricsDatasetCollection" MetricsObject <|-- MetricsDataset + click MetricsDataset href "../MetricsDataset" MetricsObject <|-- Image + click Image href "../Image" + MetricsObject <|-- Channel + click Channel href "../Channel" MetricsObject <|-- Roi + click Roi href "../Roi" MetricsObject <|-- KeyValues + click KeyValues href "../KeyValues" MetricsObject <|-- Tag + click Tag href "../Tag" MetricsObject <|-- Table + click Table href "../Table" MetricsObject : data_reference - MetricsObject --> DataReference : data_reference + + + + MetricsObject --> "0..1" DataReference : data_reference + click DataReference href "../DataReference" + MetricsObject : description MetricsObject : linked_references - MetricsObject --> DataReference : linked_references + + + + MetricsObject --> "*" DataReference : linked_references + click DataReference href "../DataReference" + MetricsObject : name @@ -242,6 +264,7 @@

    Inheritance

  • MetricsDatasetCollection
  • MetricsDataset
  • Image
    • +
  • Channel
  • Roi
  • KeyValues
  • Tag
    • @@ -270,7 +293,7 @@

    Slots

    linked_references -0..*
    DataReference +*
    DataReference A list of linked references direct @@ -327,21 +350,21 @@

    Direct

    description: A reference to the data from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - MetricsObject range: DataReference required: false + multivalued: false linked_references: name: linked_references description: A list of linked references from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true domain_of: - MetricsObject range: DataReference required: false + multivalued: true inlined: true inlined_as_list: true @@ -360,25 +383,25 @@

    Induced

    description: A reference to the data from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: data_reference owner: MetricsObject domain_of: - MetricsObject range: DataReference required: false + multivalued: false linked_references: name: linked_references description: A list of linked references from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: linked_references owner: MetricsObject domain_of: - MetricsObject range: DataReference required: false + multivalued: true inlined: true inlined_as_list: true name: @@ -386,7 +409,6 @@

    Induced

    description: The human readable name of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: name owner: MetricsObject domain_of: @@ -394,12 +416,12 @@

    Induced

    - Experimenter range: string required: false + multivalued: false description: name: description description: A human readable description of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: description owner: MetricsObject domain_of: @@ -407,6 +429,7 @@

    Induced

    - Tag range: string required: false + multivalued: false     @@ -435,5 +458,7 @@

    Induced

    - + \ No newline at end of file diff --git a/MetricsOutput/index.html b/MetricsOutput/index.html index 36b25567..80f7532c 100644 --- a/MetricsOutput/index.html +++ b/MetricsOutput/index.html @@ -7,7 +7,7 @@ - + Class: MetricsOutput - microscopemetrics-schema @@ -212,14 +212,20 @@

    Class: MetricsOutput

    URI: microscopemetrics_schema:MetricsOutput

    classDiagram class MetricsOutput + click MetricsOutput href "../MetricsOutput" MetricsOutput <|-- FieldIlluminationOutput + click FieldIlluminationOutput href "../FieldIlluminationOutput" MetricsOutput <|-- PSFBeadsOutput - MetricsOutput <|-- ArgolightBOutput - MetricsOutput <|-- ArgolightEOutput + click PSFBeadsOutput href "../PSFBeadsOutput" MetricsOutput : comment - MetricsOutput --> Comment : comment + + + + MetricsOutput --> "0..1" Comment : comment + click Comment href "../Comment" + MetricsOutput : errors @@ -233,6 +239,10 @@

    Class: MetricsOutput

    MetricsOutput : processing_version + MetricsOutput : validated + + MetricsOutput : validation_datetime + MetricsOutput : warnings @@ -242,8 +252,6 @@

    Inheritance

  • MetricsOutput
    • @@ -272,13 +280,13 @@

    Slots

    processing_entity -0..*
    String +*
    String The entity that processed the dataset direct processing_datetime -1..1
    datetime +1
    datetime The datetime of the processing by microscope-metrics direct @@ -290,17 +298,29 @@

    Slots

    warnings -0..*
    String +*
    String The warnings of the processing by microscope-metrics direct errors -0..*
    String +*
    String The errors of the processing by microscope-metrics direct +validated +1
    Boolean +Has the dataset been validated by a human +direct + + +validation_datetime +0..1
    datetime +The datetime of the validation +direct + + comment 0..1
    Comment A human readable comment about the dataset @@ -365,81 +385,102 @@

    Direct

    description: The application used to process the dataset from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true domain_of: - MetricsOutput range: string required: true + multivalued: true processing_version: name: processing_version description: The version of the application used to process the dataset from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true domain_of: - MetricsOutput range: string required: true + multivalued: true processing_entity: name: processing_entity description: The entity that processed the dataset from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true domain_of: - MetricsOutput range: string required: false + multivalued: true processing_datetime: name: processing_datetime description: The datetime of the processing by microscope-metrics from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - MetricsOutput range: datetime required: true + multivalued: false processing_log: name: processing_log description: The log of the processing by microscope-metrics from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - MetricsOutput range: string required: false + multivalued: false warnings: name: warnings description: The warnings of the processing by microscope-metrics from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true domain_of: - MetricsOutput range: string required: false + multivalued: true errors: name: errors description: The errors of the processing by microscope-metrics from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true domain_of: - MetricsOutput range: string required: false + multivalued: true + validated: + name: validated + description: Has the dataset been validated by a human + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema + rank: 1000 + ifabsent: 'False' + domain_of: + - MetricsOutput + range: boolean + required: true + multivalued: false + validation_datetime: + name: validation_datetime + description: The datetime of the validation + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema + rank: 1000 + domain_of: + - MetricsOutput + range: datetime + required: false + multivalued: false comment: name: comment description: A human readable comment about the dataset from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false domain_of: - MetricsOutput range: Comment required: false + multivalued: false     @@ -455,97 +496,122 @@

    Induced

    description: The application used to process the dataset from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: processing_application owner: MetricsOutput domain_of: - MetricsOutput range: string required: true + multivalued: true processing_version: name: processing_version description: The version of the application used to process the dataset from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: processing_version owner: MetricsOutput domain_of: - MetricsOutput range: string required: true + multivalued: true processing_entity: name: processing_entity description: The entity that processed the dataset from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: processing_entity owner: MetricsOutput domain_of: - MetricsOutput range: string required: false + multivalued: true processing_datetime: name: processing_datetime description: The datetime of the processing by microscope-metrics from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: processing_datetime owner: MetricsOutput domain_of: - MetricsOutput range: datetime required: true + multivalued: false processing_log: name: processing_log description: The log of the processing by microscope-metrics from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: processing_log owner: MetricsOutput domain_of: - MetricsOutput range: string required: false + multivalued: false warnings: name: warnings description: The warnings of the processing by microscope-metrics from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: warnings owner: MetricsOutput domain_of: - MetricsOutput range: string required: false + multivalued: true errors: name: errors description: The errors of the processing by microscope-metrics from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: errors owner: MetricsOutput domain_of: - MetricsOutput range: string required: false + multivalued: true + validated: + name: validated + description: Has the dataset been validated by a human + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema + rank: 1000 + ifabsent: 'False' + alias: validated + owner: MetricsOutput + domain_of: + - MetricsOutput + range: boolean + required: true + multivalued: false + validation_datetime: + name: validation_datetime + description: The datetime of the validation + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema + rank: 1000 + alias: validation_datetime + owner: MetricsOutput + domain_of: + - MetricsOutput + range: datetime + required: false + multivalued: false comment: name: comment description: A human readable comment about the dataset from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: comment owner: MetricsOutput domain_of: - MetricsOutput range: Comment required: false + multivalued: false @@ -574,5 +640,7 @@

    Induced

    - + \ No newline at end of file diff --git a/Microscope/index.html b/Microscope/index.html index 510763d6..533c2864 100644 --- a/Microscope/index.html +++ b/Microscope/index.html @@ -7,7 +7,7 @@ - + Class: Microscope - microscopemetrics-schema @@ -209,21 +209,38 @@

    Class: Microscope

    URI: microscopemetrics_schema:Microscope

    classDiagram class Microscope + click Microscope href "../Microscope" MetricsObject <|-- Microscope + click MetricsObject href "../MetricsObject" Microscope : comments - Microscope --> Comment : comments + + + + Microscope --> "*" Comment : comments + click Comment href "../Comment" + Microscope : data_reference - Microscope --> DataReference : data_reference + + + + Microscope --> "0..1" DataReference : data_reference + click DataReference href "../DataReference" + Microscope : description Microscope : linked_references - Microscope --> DataReference : linked_references + + + + Microscope --> "*" DataReference : linked_references + click DataReference href "../DataReference" + Microscope : manufacturer @@ -235,7 +252,12 @@

    Class: Microscope

    Microscope : type - Microscope --> MicroscopeTypeEnum : type + + + + Microscope --> "0..1" MicroscopeTypeEnum : type + click MicroscopeTypeEnum href "../MicroscopeTypeEnum" +
    @@ -286,7 +308,7 @@

    Slots

    comments -0..*
    Comment +*
    Comment A list of comments linked to the microscope direct @@ -298,7 +320,7 @@

    Slots

    linked_references -0..*
    DataReference +*
    DataReference A list of linked references MetricsObject @@ -351,18 +373,6 @@

    Usages

    range Microscope - -ArgolightBDataset -microscope -range -Microscope - - -ArgolightEDataset -microscope -range -Microscope -

    Identifier and Mapping Information

    @@ -405,7 +415,6 @@

    Direct

    rank: 1000 domain_of: - Microscope - - Sample range: MicroscopeTypeEnum required: false manufacturer: @@ -415,6 +424,7 @@

    Direct

    rank: 1000 domain_of: - Microscope + - Sample range: string required: false model: @@ -440,11 +450,11 @@

    Direct

    description: A list of comments linked to the microscope from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true domain_of: - Microscope range: Comment required: false + multivalued: true     @@ -464,7 +474,6 @@

    Induced

    owner: Microscope domain_of: - Microscope - - Sample range: MicroscopeTypeEnum required: false manufacturer: @@ -476,6 +485,7 @@

    Induced

    owner: Microscope domain_of: - Microscope + - Sample range: string required: false model: @@ -505,37 +515,37 @@

    Induced

    description: A list of comments linked to the microscope from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: comments owner: Microscope domain_of: - Microscope range: Comment required: false + multivalued: true data_reference: name: data_reference description: A reference to the data from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: data_reference owner: Microscope domain_of: - MetricsObject range: DataReference required: false + multivalued: false linked_references: name: linked_references description: A list of linked references from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: linked_references owner: Microscope domain_of: - MetricsObject range: DataReference required: false + multivalued: true inlined: true inlined_as_list: true name: @@ -543,7 +553,6 @@

    Induced

    description: The human readable name of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: name owner: Microscope domain_of: @@ -551,12 +560,12 @@

    Induced

    - Experimenter range: string required: false + multivalued: false description: name: description description: A human readable description of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: description owner: Microscope domain_of: @@ -564,6 +573,7 @@

    Induced

    - Tag range: string required: false + multivalued: false     @@ -592,5 +602,7 @@

    Induced

    - + \ No newline at end of file diff --git a/MicroscopeCollection/index.html b/MicroscopeCollection/index.html index 1bb9d5e7..ef42a790 100644 --- a/MicroscopeCollection/index.html +++ b/MicroscopeCollection/index.html @@ -7,7 +7,7 @@ - + Class: MicroscopeCollection - microscopemetrics-schema @@ -199,9 +199,15 @@

    Class: MicroscopeCollection

    URI: microscopemetrics_schema:MicroscopeCollection

    classDiagram class MicroscopeCollection + click MicroscopeCollection href "../MicroscopeCollection" MicroscopeCollection : microscopes - MicroscopeCollection --> Microscope : microscopes + + + + MicroscopeCollection --> "1..*" Microscope : microscopes + click Microscope href "../Microscope" +
    @@ -262,11 +268,11 @@

    Direct

    description: The microscopes of the collection from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true domain_of: - MicroscopeCollection range: Microscope required: true + multivalued: true     @@ -281,13 +287,13 @@

    Induced

    description: The microscopes of the collection from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: microscopes owner: MicroscopeCollection domain_of: - MicroscopeCollection range: Microscope required: true + multivalued: true @@ -316,5 +322,7 @@

    Induced

    - + \ No newline at end of file diff --git a/MicroscopeTypeEnum/index.html b/MicroscopeTypeEnum/index.html index e863304f..8c3a02ea 100644 --- a/MicroscopeTypeEnum/index.html +++ b/MicroscopeTypeEnum/index.html @@ -11,7 +11,7 @@ - + diff --git a/NamedObject/index.html b/NamedObject/index.html index 9da631fc..41abe59c 100644 --- a/NamedObject/index.html +++ b/NamedObject/index.html @@ -7,7 +7,7 @@ - + Class: NamedObject - microscopemetrics-schema @@ -207,12 +207,17 @@

    Class: NamedObject

    URI: microscopemetrics_schema:NamedObject

    classDiagram class NamedObject + click NamedObject href "../NamedObject" NamedObject <|-- MetricsObject + click MetricsObject href "../MetricsObject" NamedObject <|-- Sample + click Sample href "../Sample" NamedObject <|-- Protocol - NamedObject <|-- Channel + click Protocol href "../Protocol" NamedObject <|-- Column + click Column href "../Column" NamedObject <|-- Shape + click Shape href "../Shape" NamedObject : description @@ -226,7 +231,6 @@

    Inheritance

  • MetricsObject
  • Sample
  • Protocol
    • -
  • Channel
  • Column
  • Shape
    • @@ -307,7 +311,6 @@

    Induced

    description: The human readable name of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: name owner: NamedObject domain_of: @@ -315,12 +318,12 @@

    Induced

    - Experimenter range: string required: false + multivalued: false description: name: description description: A human readable description of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: description owner: NamedObject domain_of: @@ -328,6 +331,7 @@

    Induced

    - Tag range: string required: false + multivalued: false @@ -356,5 +360,7 @@

    Induced

    - + \ No newline at end of file diff --git a/Ncname/index.html b/Ncname/index.html index b45ad478..6bb9abce 100644 --- a/Ncname/index.html +++ b/Ncname/index.html @@ -11,7 +11,7 @@ - + diff --git a/Nodeidentifier/index.html b/Nodeidentifier/index.html index 4424edf0..de475375 100644 --- a/Nodeidentifier/index.html +++ b/Nodeidentifier/index.html @@ -11,7 +11,7 @@ - + diff --git a/OMEROObjectTypeEnum/index.html b/OMEROObjectTypeEnum/index.html index 4ed79d37..2ee77291 100644 --- a/OMEROObjectTypeEnum/index.html +++ b/OMEROObjectTypeEnum/index.html @@ -11,7 +11,7 @@ - + @@ -335,6 +335,11 @@

    Permissible Values

    An image +CHANNEL +None +A channel + + DATASET None A dataset @@ -417,6 +422,9 @@

    LinkML Source

    IMAGE: text: IMAGE description: An image + CHANNEL: + text: CHANNEL + description: A channel DATASET: text: DATASET description: A dataset diff --git a/Objectidentifier/index.html b/Objectidentifier/index.html index 78444c0c..08206060 100644 --- a/Objectidentifier/index.html +++ b/Objectidentifier/index.html @@ -11,7 +11,7 @@ - + diff --git a/ArgolightEInput/index.html b/PSFBeads/index.html similarity index 72% rename from ArgolightEInput/index.html rename to PSFBeads/index.html index 4f10194a..275b2be4 100644 --- a/ArgolightEInput/index.html +++ b/PSFBeads/index.html @@ -5,10 +5,10 @@ - + - -Class: ArgolightEInput - microscopemetrics-schema + +Class: PSFBeads - microscopemetrics-schema @@ -21,7 +21,7 @@
    - + Skip to content
    @@ -45,7 +45,7 @@
    - Class: ArgolightEInput + Class: PSFBeads
    @@ -201,35 +201,44 @@
    - + -

    Class: ArgolightEInput

    -

    URI: microscopemetrics_schema:ArgolightEInput

    +

    Class: PSFBeads

    +

    A sample of sub-resolution sized beads used to measure the PSF of a microscope.

    +

    URI: microscopemetrics_schema:PSFBeads

    classDiagram - class ArgolightEInput - MetricsInput <|-- ArgolightEInput + class PSFBeads + click PSFBeads href "../PSFBeads" + Sample <|-- PSFBeads + click Sample href "../Sample" - ArgolightEInput : argolight_e_image + PSFBeads : bead_diameter_micron - ArgolightEInput --> Image : argolight_e_image + PSFBeads : description - ArgolightEInput : bit_depth + PSFBeads : manufacturer - ArgolightEInput : measured_band + PSFBeads : name - ArgolightEInput : orientation_axis + PSFBeads : protocol - ArgolightEInput : prominence_threshold - ArgolightEInput : saturation_threshold + + + PSFBeads --> "1" Protocol : protocol + click Protocol href "../Protocol" +

    Inheritance

    - + \ No newline at end of file diff --git a/PSFBeadsDataset/index.html b/PSFBeadsDataset/index.html index 4533dc28..d90ab26f 100644 --- a/PSFBeadsDataset/index.html +++ b/PSFBeadsDataset/index.html @@ -7,7 +7,7 @@ - + Class: PSFBeadsDataset - microscopemetrics-schema @@ -204,43 +204,89 @@

    Class: PSFBeadsDataset

    URI: microscopemetrics_schema:PSFBeadsDataset

    classDiagram class PSFBeadsDataset + click PSFBeadsDataset href "../PSFBeadsDataset" MetricsDataset <|-- PSFBeadsDataset + click MetricsDataset href "../MetricsDataset" PSFBeadsDataset : acquisition_datetime PSFBeadsDataset : data_reference - PSFBeadsDataset --> DataReference : data_reference + + + + PSFBeadsDataset --> "0..1" DataReference : data_reference + click DataReference href "../DataReference" + PSFBeadsDataset : description PSFBeadsDataset : experimenter - PSFBeadsDataset --> Experimenter : experimenter - PSFBeadsDataset : input - PSFBeadsDataset --> PSFBeadsInput : input + + PSFBeadsDataset --> "0..1" Experimenter : experimenter + click Experimenter href "../Experimenter" + + + PSFBeadsDataset : input_data + + + + + PSFBeadsDataset --> "0..1" PSFBeadsInputData : input_data + click PSFBeadsInputData href "../PSFBeadsInputData" + + + PSFBeadsDataset : input_parameters + + + + + PSFBeadsDataset --> "0..1" PSFBeadsInputParameters : input_parameters + click PSFBeadsInputParameters href "../PSFBeadsInputParameters" + PSFBeadsDataset : linked_references - PSFBeadsDataset --> DataReference : linked_references + + + + PSFBeadsDataset --> "*" DataReference : linked_references + click DataReference href "../DataReference" + PSFBeadsDataset : microscope - PSFBeadsDataset --> Microscope : microscope + + + + PSFBeadsDataset --> "1" Microscope : microscope + click Microscope href "../Microscope" + PSFBeadsDataset : name PSFBeadsDataset : output - PSFBeadsDataset --> PSFBeadsOutput : output + + + + PSFBeadsDataset --> "0..1" PSFBeadsOutput : output + click PSFBeadsOutput href "../PSFBeadsOutput" + PSFBeadsDataset : processed PSFBeadsDataset : sample - PSFBeadsDataset --> Sample : sample + + + + PSFBeadsDataset --> "0..1" PSFBeads : sample + click PSFBeads href "../PSFBeads" +
    @@ -269,8 +315,14 @@

    Slots

    -input -0..1
    PSFBeadsInput +input_data +0..1
    PSFBeadsInputData + +direct + + +input_parameters +0..1
    PSFBeadsInputParameters direct @@ -281,15 +333,15 @@

    Slots

    direct -microscope -1..1
    Microscope -The microscope that was used to acquire the dataset -MetricsDataset +sample +0..1
    PSFBeads + +direct -sample -0..1
    Sample -The sample that was imaged +microscope +1
    Microscope +The microscope that was used to acquire the dataset MetricsDataset @@ -306,7 +358,7 @@

    Slots

    processed -1..1
    Boolean +1
    Boolean Has the dataset been processed by microscope-metrics MetricsDataset @@ -318,7 +370,7 @@

    Slots

    linked_references -0..*
    DataReference +*
    DataReference A list of linked references MetricsObject @@ -369,26 +421,38 @@

    Direct

    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema is_a: MetricsDataset attributes: - input: - name: input - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/psf_beads_schema + input_data: + name: input_data + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads_schema + domain_of: + - MetricsDataset + - FieldIlluminationDataset + - PSFBeadsDataset + range: PSFBeadsInputData + input_parameters: + name: input_parameters + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads_schema domain_of: - MetricsDataset - FieldIlluminationDataset - PSFBeadsDataset - - ArgolightBDataset - - ArgolightEDataset - range: PSFBeadsInput + range: PSFBeadsInputParameters output: name: output - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/psf_beads_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads_schema domain_of: - MetricsDataset - FieldIlluminationDataset - PSFBeadsDataset - - ArgolightBDataset - - ArgolightEDataset range: PSFBeadsOutput + sample: + name: sample + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads_schema + domain_of: + - MetricsDataset + - FieldIlluminationDataset + - PSFBeadsDataset + range: PSFBeads     @@ -399,82 +463,83 @@

    Induced

    from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema is_a: MetricsDataset attributes: - input: - name: input - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/psf_beads_schema - alias: input + input_data: + name: input_data + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads_schema + alias: input_data + owner: PSFBeadsDataset + domain_of: + - MetricsDataset + - FieldIlluminationDataset + - PSFBeadsDataset + range: PSFBeadsInputData + input_parameters: + name: input_parameters + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads_schema + alias: input_parameters owner: PSFBeadsDataset domain_of: - MetricsDataset - FieldIlluminationDataset - PSFBeadsDataset - - ArgolightBDataset - - ArgolightEDataset - range: PSFBeadsInput + range: PSFBeadsInputParameters output: name: output - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/samples/psf_beads_schema + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads_schema alias: output owner: PSFBeadsDataset domain_of: - MetricsDataset - FieldIlluminationDataset - PSFBeadsDataset - - ArgolightBDataset - - ArgolightEDataset range: PSFBeadsOutput + sample: + name: sample + from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/analyses/psf_beads_schema + alias: sample + owner: PSFBeadsDataset + domain_of: + - MetricsDataset + - FieldIlluminationDataset + - PSFBeadsDataset + range: PSFBeads microscope: name: microscope description: The microscope that was used to acquire the dataset from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 - multivalued: false alias: microscope owner: PSFBeadsDataset domain_of: - MetricsDataset range: Microscope required: true - sample: - name: sample - description: The sample that was imaged - from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 multivalued: false - alias: sample - owner: PSFBeadsDataset - domain_of: - - MetricsDataset - range: Sample experimenter: name: experimenter description: The experimenter that performed the imaging experiment from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 - multivalued: false alias: experimenter owner: PSFBeadsDataset domain_of: - MetricsDataset range: Experimenter + multivalued: false acquisition_datetime: name: acquisition_datetime description: The datetime of the acquisition from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema - rank: 1000 - multivalued: false alias: acquisition_datetime owner: PSFBeadsDataset domain_of: - MetricsDataset - Image range: datetime + multivalued: false processed: name: processed description: Has the dataset been processed by microscope-metrics from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false ifabsent: 'False' alias: processed owner: PSFBeadsDataset @@ -482,30 +547,31 @@

    Induced

    - MetricsDataset range: boolean required: true + multivalued: false data_reference: name: data_reference description: A reference to the data from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: false alias: data_reference owner: PSFBeadsDataset domain_of: - MetricsObject range: DataReference required: false + multivalued: false linked_references: name: linked_references description: A list of linked references from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema/core_schema rank: 1000 - multivalued: true alias: linked_references owner: PSFBeadsDataset domain_of: - MetricsObject range: DataReference required: false + multivalued: true inlined: true inlined_as_list: true name: @@ -513,7 +579,6 @@

    Induced

    description: The human readable name of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: name owner: PSFBeadsDataset domain_of: @@ -521,12 +586,12 @@

    Induced

    - Experimenter range: string required: false + multivalued: false description: name: description description: A human readable description of an entity from_schema: https://MontpellierRessourcesImagerie.github.io/microscopemetrics-schema rank: 1000 - multivalued: false alias: description owner: PSFBeadsDataset domain_of: @@ -534,6 +599,7 @@

    Induced

    - Tag range: string required: false + multivalued: false     @@ -562,5 +628,7 @@

    Induced

    - + \ No newline at end of file diff --git a/ColumnSeries/index.html b/PSFBeadsInputData/index.html similarity index 84% rename from ColumnSeries/index.html rename to PSFBeadsInputData/index.html index dfb9e0eb..44260879 100644 --- a/ColumnSeries/index.html +++ b/PSFBeadsInputData/index.html @@ -5,10 +5,10 @@ - + - -Class: ColumnSeries - microscopemetrics-schema + +Class: PSFBeadsInputData - microscopemetrics-schema @@ -21,7 +21,7 @@
    - + Skip to content
    @@ -45,7 +45,7 @@
    - Class: ColumnSeries + Class: PSFBeadsInputData
    @@ -142,6 +142,11 @@