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Capture new layout of HCS specification
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sbesson committed Nov 8, 2020
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Expand Up @@ -67,12 +67,16 @@ multiple levels of resolutions and optionally associated labels.
The following layout should describe the hierarchy for a high-content screening
dataset. There are exactly four levels of hierarchies above the images:

- the top-level group defines the plate, it MUST implement the plate
- the top-level group defines a single plate and MUST implement the plate
specification defined below
- the second group defines all acquisitions performed on a single plate. If
- the second group defines all acquisitions performed on the plate. If
only one acquisition was performed, a single group must be used.
- the third group defines all the well rows available for an acquisition
- the fourth group defines all the well columns available for a given well row
- the third group defines all the rows available for an acquisition. The group
name must match the name of one of the row objects defined in the plate
metadata.
- the fourth group defines all the wells available for a given row. The group
name must match the name of one of the columd objects defined in the plate
metadata. The well group MUST implement the well specification defined below
- the fifth group defined all the individual fields of views for a given well.
The fields of views are images, SHOULD implement the "multiscales"
specification, MAY implement the "omero" specification and MAY contain
Expand All @@ -98,9 +102,9 @@ dataset. There are exactly four levels of hierarchies above the images:
│ │ │
│ │ ├── 1 # First column of row A
│ │ │ ├── .zgroup
│ │ │ ├── .zattrs
│ │ │ ├── .zattrs # Implements "well" specification
│ │ │ │
│ │ │ ├── Field_1 # First field of view of well A1
│ │ │ ├── 0 # First field of view of well A1
│ │ │ │ │
│ │ │ │ ├── .zgroup
│ │ │ │ ├── .zattrs # Implements "multiscales", "omero"
Expand All @@ -109,7 +113,7 @@ dataset. There are exactly four levels of hierarchies above the images:
│ │ │ │ ├── n
│ │ │ │ └── labels
│ │ │ ├── ... # Fields of view
│ │ │ └── Field_m
│ │ │ └── m
│ │ ├── ... # Columns
│ │ └── 12
│ ├── ... # Rows
Expand Down Expand Up @@ -250,72 +254,93 @@ For high-content screening datasets, the plate layout can be found under the cus
<dl>
<dt><strong>name</strong></dt>
<dd>A string defining the name of the plate.</dd>
<dt><strong>plateAcquisitions</strong></dt>
<dt><strong>acquisitions</strong></dt>
<dd>A list of JSON objects defining the acquisitions for a given plate.
Each acquisition object MUST contain a `path` key identifying the path
to the acquisition group.</dd>
to the acquisition subgroup.</dd>
<dt><strong>rows</strong></dt>
<dd>An integer defining the number of rows i.e. the first dimension of
a two-dimensional array of wells.</dd>
<dt><strong>row_names</strong></dt>
<dd>A list of strings defining the names of the rows</dd>
<dt><strong>rows</strong></dt>
<dd>An integer defining the number of columns i.e. the first dimension of
a two-dimensional array of wells.</dd>
<dt><strong>column_names</strong></dt>
<dd>A list of strings defining the names of the columns</dd>
<dt><strong>images</strong></dt>
<dd>A list of JSON objects defining the images (or well samples) containing in the plate.
Each image object MUST contain a `path` key identifying the path to the
individual image.</dd>
<dd>A list of JSON defining the rows of the plate. Each row object defines
the properties of the row at the index of the object in the list. If
not empty, it MUST contain a `name` key specifying the row name.</dd>
<dt><strong>columns</strong></dt>
<dd>A list of JSON defining the columns of the plate. Each column object
defines the properties of the column at the index of the object in the
list. If not empty, it MUST contain a `name` key specifying the column
name.</dd>
<dt><strong>field_count</strong></dt>
<dd>An integer defining the maximum number of fields per view across all
wells.</dd>
<dt><strong>wells</strong></dt>
<dd>A list of JSON objects defining the wells of the plate. Each well object
MUST contain a `path` key identifying the path to the well subgroup.</dd>
</dl>

For example the following JSON object encodes a plate with one acquisition and
6 wells containing up to two fields of view each.
For example the following JSON object defines a plate with one acquisition and
6 wells (2 rows and 3 columns), containing up to three fields of view each.

```json
"plate":
{
"plate": {
"acquisitions": [{"path": "0"}],
"columns": [{"name": "1" }, {"name": "2" }, {"name": "3" }],
"field_count": 3,
"name": "test",
"rows": 2,
"columns": 3,
"row_names": ["A", "B"],
"column_names": ["1", "2", "3"],
"plateAcquisitions": [
{"path": "2020-10-10"}
],
"images": [
"rows": [{"name": "A" }, {"name": "B" }],
"wells": [
{
"path": "2020-10-10/A/1/Field_1"
"path": "2020-10-10/A/1"
},
{
"path": "2020-10-10/A/1/Field_2"
"path": "2020-10-10/A/2"
},
{
"path": "2020-10-10/A/2/Field_1"
"path": "2020-10-10/A/3"
},
{
"path": "2020-10-10/A/2/Field_2"
"path": "2020-10-10/B/1"
},
{
"path": "2020-10-10/A/3/Field_1"
"path": "2020-10-10/B/2"
},
{
"path": "2020-10-10/B/1/Field_1"
"path": "2020-10-10/B/3"
}
]
}
```

### "well" metadata

For high-content screening datasets, the metadata about all fields of views
under a given well can be found under the "well" key in the attributes of the
well group.

<dl>
<dt><strong>images</strong></dt>
<dd>A list of JSON objects defining the fields of views for a given well.
Each object MUST contain a `path` key identifying the path to the
field of view.</dd>
</dl>

For example the following JSON object defines a well with three fields of
views:

```json
"well": {
"images": [
{
"path": "0"
},
{
"path": "2020-10-10/B/2/Field_1"
"path": "1"
},
{
"path": "2020-10-10/B/3/Field_1"
}
"path": "2"
},
]
}
```




| Revision | Date | Description |
| ---------- | ------------ | ------------------------------------------ |
| 0.1.3-dev5 | TBD. | Add the HCS specification |
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