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[ENH] BEP031: Microscopy #881

Merged
merged 76 commits into from
Jan 18, 2022
Merged

[ENH] BEP031: Microscopy #881

merged 76 commits into from
Jan 18, 2022

Commits on Sep 16, 2021

  1. Initial commit adding Microscopy related files

    @mariehbourget
    mariehbourget committed Sep 16, 2021
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  2. Add Link descriptions and fix md formatting

    @mariehbourget
    mariehbourget committed Sep 16, 2021
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Commits on Sep 20, 2021

  1. Fix md formatting

    @mariehbourget
    mariehbourget committed Sep 20, 2021
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Commits on Sep 28, 2021

  1. Move "chunk" entity at the end of filename before modality_suffix

    @mariehbourget
    mariehbourget committed Sep 28, 2021
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Commits on Sep 30, 2021

  1. Add link to OME-TIFF dataset

    @mariehbourget
    mariehbourget committed Sep 30, 2021
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  2. Update src/04-modality-specific-files/10-microscopy.md 

    Typo

Co-authored-by: Chris Markiewicz <[email protected]>
    @mariehbourget @effigies
    mariehbourget and effigies authored Sep 30, 2021
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Commits on Oct 1, 2021

  1. Apply suggestions from code review 

    Co-authored-by: Chris Markiewicz <[email protected]>
    @mariehbourget @effigies
    mariehbourget and effigies authored Oct 1, 2021
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  2. Update "TissueDeformationScaling" field and JSON example

    @mariehbourget
    mariehbourget committed Oct 1, 2021
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  3. Update "uCT" suffix in schema/datatypes/microscopy.yaml

    @mariehbourget
    mariehbourget committed Oct 1, 2021
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  4. Add res-label example

    @mariehbourget
    mariehbourget committed Oct 1, 2021
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Commits on Oct 8, 2021

  1. Add "mm" and "nm" to PixelSizeUnits

    @mariehbourget
    mariehbourget committed Oct 8, 2021
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Commits on Oct 15, 2021

  1. Update "Recommended participant data" after merge of PR #816

    @mariehbourget
    mariehbourget committed Oct 15, 2021
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Commits on Oct 16, 2021

  1. Resolve conflict with master for entities.yaml

    @mariehbourget
    mariehbourget committed Oct 16, 2021
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  2. Merge branch 'master' into bep031

    @mariehbourget
    mariehbourget committed Oct 16, 2021
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  3. Update entities.yaml in objects and rules schema folders

    @mariehbourget
    mariehbourget committed Oct 16, 2021
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  4. Update microscopy.yaml datatypes rules schema folder

    @mariehbourget
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Commits on Oct 27, 2021

  1. Apply suggestions from code review 

    Co-authored-by: Remi Gau <[email protected]>
    @mariehbourget @Remi-Gau
    mariehbourget and Remi-Gau authored Oct 27, 2021
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  2. Fix md formatting

    @mariehbourget
    mariehbourget committed Oct 27, 2021
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Commits on Oct 28, 2021

  1. Make protocols.io an example in SampleExtractionProtocol and 

    ImageAcquisitionProtocol
    @mariehbourget
    mariehbourget committed Oct 28, 2021
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Commits on Nov 4, 2021

  1. Re-wording of chunk-index section and chunk transformation matrix is 

    recommended for ordered chunks
    @mariehbourget
    mariehbourget committed Nov 4, 2021
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  2. Fix typos

    @mariehbourget
    mariehbourget committed Nov 4, 2021
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Commits on Nov 9, 2021

  1. Fix wording

    @mariehbourget
    mariehbourget committed Nov 9, 2021
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Commits on Nov 12, 2021

  1. Fix tif extension in src/schema/rules/datatypes/microscopy.yaml

    @mariehbourget
    mariehbourget committed Nov 12, 2021
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  2. Remove duplicated text in stain-label description

    @mariehbourget
    mariehbourget committed Nov 12, 2021
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  3. Correction of the name of "Fluorescence" modality to "Fluorescence mi… 

    …croscopy"
    @mariehbourget
    mariehbourget committed Nov 12, 2021
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  4. Add figure and example for chunk transformation

    @mariehbourget
    mariehbourget committed Nov 12, 2021
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Commits on Nov 13, 2021

  1. Update src/04-modality-specific-files/10-microscopy.md 

    Co-authored-by: Julien Cohen-Adad <[email protected]>
    @mariehbourget @jcohenadad
    mariehbourget and jcohenadad authored Nov 13, 2021
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Commits on Nov 15, 2021

  1. Update README.md 

    Co-authored-by: Yaroslav Halchenko <[email protected]>
    @mariehbourget @yarikoptic
    mariehbourget and yarikoptic authored Nov 15, 2021
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  2. Add full OME-NGFF name

    @mariehbourget
    mariehbourget committed Nov 15, 2021
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  3. Correction

    @mariehbourget
    mariehbourget committed Nov 15, 2021
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  4. Fix formatting

    @mariehbourget
    mariehbourget committed Nov 15, 2021
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Commits on Nov 16, 2021

  1. Make BodyPartDetails RECOMMENDED

    @mariehbourget
    mariehbourget committed Nov 16, 2021
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  2. Update src/04-modality-specific-files/10-microscopy.md 

    Co-authored-by: Yaroslav Halchenko <[email protected]>
    @mariehbourget @yarikoptic
    mariehbourget and yarikoptic authored Nov 16, 2021
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  3. Clarify stain-label and SampleStaining text in Filename entities section

    @mariehbourget
    mariehbourget committed Nov 16, 2021
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  4. Update examples with real modality_suffix and file extensions

    @mariehbourget
    mariehbourget committed Nov 16, 2021
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  5. Clarify text of chunk-index and chunk transformation

    @mariehbourget
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  6. Update BodyPartDetailsOntology as URI

    @mariehbourget
    mariehbourget committed Nov 16, 2021
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  7. Correction to SampleEnvironment values

    @mariehbourget
    mariehbourget committed Nov 16, 2021
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  8. Fix md formatting

    @mariehbourget
    mariehbourget committed Nov 16, 2021
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Commits on Nov 18, 2021

  1. Add mention that "session" is optional

    @mariehbourget
    mariehbourget committed Nov 18, 2021
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  2. wording: replace some "can" with "MAY" or "MUST"

    @mariehbourget
    mariehbourget committed Nov 18, 2021
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  3. Clarification on participants.tsv file

    @mariehbourget
    mariehbourget committed Nov 18, 2021
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Commits on Nov 19, 2021

  1. Correction to stain description in entities.yml

    @mariehbourget
    mariehbourget committed Nov 19, 2021
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Commits on Nov 23, 2021

  1. Update src/02-common-principles.md 

    Co-authored-by: Yaroslav Halchenko <[email protected]>
    @mariehbourget @yarikoptic
    mariehbourget and yarikoptic authored Nov 23, 2021
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  2. 10-microscpy.md: Change "microscopy" data type for "micr"

    @mariehbourget
    mariehbourget committed Nov 23, 2021
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  3. Update datatype micr.yaml in schema and fix macro in entity table

    @mariehbourget
    mariehbourget committed Nov 23, 2021
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  4. Clarify usage of samples/participants tsv/json files

    @mariehbourget
    mariehbourget committed Nov 23, 2021
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  5. Correction to "ex vivo" in JSON example

    @mariehbourget
    mariehbourget committed Nov 23, 2021
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  6. Correction samples/participants tsv/json file sections

    @mariehbourget
    mariehbourget committed Nov 23, 2021
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Commits on Nov 26, 2021

  1. Merge branch 'master' into bep031

    @mariehbourget
    mariehbourget committed Nov 26, 2021
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Commits on Nov 29, 2021

  1. Implement macros for examples

    @mariehbourget
    mariehbourget committed Nov 29, 2021
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  2. Correction: replace <modality_suffix> by <suffix>

    @mariehbourget
    mariehbourget committed Nov 29, 2021
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Commits on Nov 30, 2021

  1. Add microscopy to schema/objects/datatypes.yaml

    @mariehbourget
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  2. Add microscopy suffixes to schema/objects/suffixes.yaml

    @mariehbourget
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  3. Add microscopy to schema/rules/modalities.yaml

    @mariehbourget
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  4. Add make_filename_template MACROs

    @mariehbourget
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  5. Add make_suffix_table MACRO

    @mariehbourget
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Commits on Dec 2, 2021

  1. Add microscopy json metadata to schema/objects/metadata.yaml

    @mariehbourget
    mariehbourget committed Dec 2, 2021
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  2. Add metadata table macros to 10-microscopy.md

    @mariehbourget
    mariehbourget committed Dec 2, 2021
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  3. Adjust StationName definition in 01-magnetic-resonance-imaging-data.md

    @mariehbourget
    mariehbourget committed Dec 2, 2021
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  4. Adjust BodyPart definition in 09-positron-emission-tomography.md

    @mariehbourget
    mariehbourget committed Dec 2, 2021
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  5. Change "recording data" for "imaging data"

    @mariehbourget
    mariehbourget committed Dec 2, 2021
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  6. Remove unused link definitions

    @mariehbourget
    mariehbourget committed Dec 2, 2021
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Commits on Dec 3, 2021

  1. Clarify samples/participants sections

    @mariehbourget
    mariehbourget committed Dec 3, 2021
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  2. schema/objects/metadata.yaml: Apply review suggestions and add 

    restrictions
    @mariehbourget
    mariehbourget committed Dec 3, 2021
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  3. Address BEP031 macro requests (#945) 

    * Allow table-specific numbers of duplicate suffixes/exts to combine.

* Only combine compressed versions of extensions.
    @tsalo
    tsalo authored Dec 3, 2021
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  4. Update src/schema/objects/metadata.yaml 

    Co-authored-by: Taylor Salo <[email protected]>
    @mariehbourget @tsalo
    mariehbourget and tsalo authored Dec 3, 2021
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Commits on Dec 6, 2021

  1. Update names of bids-examples datasets

    @mariehbourget
    mariehbourget committed Dec 6, 2021
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  2. Remove comments about filename templates

    @mariehbourget
    mariehbourget committed Dec 6, 2021
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  3. Remove comments for modality suffix table

    @mariehbourget
    mariehbourget committed Dec 6, 2021
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Commits on Dec 20, 2021

  1. Apply suggestions from code review 

    Co-authored-by: Yaroslav Halchenko <[email protected]>
    @mariehbourget @yarikoptic
    mariehbourget and yarikoptic authored Dec 20, 2021
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Commits on Jan 13, 2022

  1. Update BIDS-examples link and remove commented lines

    @mariehbourget
    mariehbourget committed Jan 13, 2022
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  2. Add "samples" to src/schema/objects/top_level_files.yaml

    @mariehbourget
    mariehbourget committed Jan 13, 2022
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  3. Formatting in src/schema/objects/top_level_files.yaml

    @mariehbourget
    mariehbourget committed Jan 13, 2022
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  4. Merge remote-tracking branch 'upstream/master' into bep031

    @effigies
    effigies committed Jan 13, 2022
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Commits on Jan 17, 2022

  1. Fix link to sessions file in src/schema/objects/top_level_files.yaml

    @mariehbourget
    mariehbourget committed Jan 17, 2022
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