From c30bd4d79ee2ab908517176340a094639937ebeb Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 29 Nov 2024 21:27:52 +0000 Subject: [PATCH 1/4] Populate latest folder with copy of spec --- latest | 1 - latest/copyright.include | 4 + latest/examples/bf2raw/.config.json | 3 + latest/examples/bf2raw/image.json | 10 + latest/examples/bf2raw/plate.json | 36 + latest/examples/label_strict/.config.json | 3 + .../label_strict/colors_properties.json | 37 + .../examples/multiscales_strict/.config.json | 3 + .../multiscales_example.json | 68 ++ .../multiscales_transformations.json | 47 + latest/examples/ome/.config.json | 3 + latest/examples/ome/series-2.json | 10 + latest/examples/plate_strict/.config.json | 3 + .../examples/plate_strict/plate_2wells.json | 97 ++ .../examples/plate_strict/plate_6wells.json | 78 ++ latest/examples/well_strict/.config.json | 3 + latest/examples/well_strict/well_2fields.json | 21 + latest/examples/well_strict/well_4fields.json | 29 + latest/header.include | 34 + latest/index.bs | 718 ++++++++++++ latest/schemas/_version.schema | 10 + latest/schemas/bf2raw.schema | 32 + latest/schemas/image.schema | 268 +++++ latest/schemas/label.schema | 91 ++ latest/schemas/ome.schema | 33 + latest/schemas/ome_zarr.schema | 24 + latest/schemas/plate.schema | 153 +++ latest/schemas/strict_image.schema | 25 + latest/schemas/strict_label.schema | 21 + latest/schemas/strict_plate.schema | 31 + latest/schemas/strict_well.schema | 8 + latest/schemas/well.schema | 56 + latest/tests/image_suite.json | 1040 +++++++++++++++++ latest/tests/label_suite.json | 158 +++ latest/tests/plate_suite.json | 883 ++++++++++++++ latest/tests/strict_image_suite.json | 341 ++++++ latest/tests/strict_label_suite.json | 18 + latest/tests/strict_plate_suite.json | 171 +++ latest/tests/strict_well_suite.json | 41 + latest/tests/test_validation.py | 125 ++ latest/tests/well_suite.json | 80 ++ latest/tox.ini | 10 + 42 files changed, 4826 insertions(+), 1 deletion(-) delete mode 120000 latest create mode 100644 latest/copyright.include create mode 100644 latest/examples/bf2raw/.config.json create mode 100644 latest/examples/bf2raw/image.json create mode 100644 latest/examples/bf2raw/plate.json create mode 100644 latest/examples/label_strict/.config.json create mode 100644 latest/examples/label_strict/colors_properties.json create mode 100644 latest/examples/multiscales_strict/.config.json create mode 100644 latest/examples/multiscales_strict/multiscales_example.json create mode 100644 latest/examples/multiscales_strict/multiscales_transformations.json create mode 100644 latest/examples/ome/.config.json create mode 100644 latest/examples/ome/series-2.json create mode 100644 latest/examples/plate_strict/.config.json create mode 100644 latest/examples/plate_strict/plate_2wells.json create mode 100644 latest/examples/plate_strict/plate_6wells.json create mode 100644 latest/examples/well_strict/.config.json create mode 100644 latest/examples/well_strict/well_2fields.json create mode 100644 latest/examples/well_strict/well_4fields.json create mode 100644 latest/header.include create mode 100644 latest/index.bs create mode 100644 latest/schemas/_version.schema create mode 100644 latest/schemas/bf2raw.schema create mode 100644 latest/schemas/image.schema create mode 100644 latest/schemas/label.schema create mode 100644 latest/schemas/ome.schema create mode 100644 latest/schemas/ome_zarr.schema create mode 100644 latest/schemas/plate.schema create mode 100644 latest/schemas/strict_image.schema create mode 100644 latest/schemas/strict_label.schema create mode 100644 latest/schemas/strict_plate.schema create mode 100644 latest/schemas/strict_well.schema create mode 100644 latest/schemas/well.schema create mode 100644 latest/tests/image_suite.json create mode 100644 latest/tests/label_suite.json create mode 100644 latest/tests/plate_suite.json create mode 100644 latest/tests/strict_image_suite.json create mode 100644 latest/tests/strict_label_suite.json create mode 100644 latest/tests/strict_plate_suite.json create mode 100644 latest/tests/strict_well_suite.json create mode 100644 latest/tests/test_validation.py create mode 100644 latest/tests/well_suite.json create mode 100644 latest/tox.ini diff --git a/latest b/latest deleted file mode 120000 index ea2303bc..00000000 --- a/latest +++ /dev/null @@ -1 +0,0 @@ -0.5 \ No newline at end of file diff --git a/latest/copyright.include b/latest/copyright.include new file mode 100644 index 00000000..f0def708 --- /dev/null +++ b/latest/copyright.include @@ -0,0 +1,4 @@ +Copyright © 2020-[YEAR] +OME® +(U. Dundee). +OME trademark rules apply. diff --git a/latest/examples/bf2raw/.config.json b/latest/examples/bf2raw/.config.json new file mode 100644 index 00000000..2525328c --- /dev/null +++ b/latest/examples/bf2raw/.config.json @@ -0,0 +1,3 @@ +{ + "schema": "schemas/bf2raw.schema" +} diff --git a/latest/examples/bf2raw/image.json b/latest/examples/bf2raw/image.json new file mode 100644 index 00000000..8fda1fd2 --- /dev/null +++ b/latest/examples/bf2raw/image.json @@ -0,0 +1,10 @@ +{ + "zarr_format": 3, + "node_type": "group", + "attributes": { + "ome": { + "version": "0.5", + "bioformats2raw.layout": 3 + } + } +} diff --git a/latest/examples/bf2raw/plate.json b/latest/examples/bf2raw/plate.json new file mode 100644 index 00000000..ef1ac0a7 --- /dev/null +++ b/latest/examples/bf2raw/plate.json @@ -0,0 +1,36 @@ +{ + "zarr_format": 3, + "node_type": "group", + "attributes": { + "ome": { + "version": "0.5", + "bioformats2raw.layout": 3, + "plate": { + "columns": [ + { + "name": "1" + } + ], + "name": "Plate Name 0", + "wells": [ + { + "path": "A/1", + "rowIndex": 0, + "columnIndex": 0 + } + ], + "field_count": 1, + "rows": [ + { + "name": "A" + } + ], + "acquisitions": [ + { + "id": 0 + } + ] + } + } + } +} diff --git a/latest/examples/label_strict/.config.json b/latest/examples/label_strict/.config.json new file mode 100644 index 00000000..e7329dc9 --- /dev/null +++ b/latest/examples/label_strict/.config.json @@ -0,0 +1,3 @@ +{ + "schema": "schemas/strict_label.schema" +} diff --git a/latest/examples/label_strict/colors_properties.json b/latest/examples/label_strict/colors_properties.json new file mode 100644 index 00000000..fa1f4cd6 --- /dev/null +++ b/latest/examples/label_strict/colors_properties.json @@ -0,0 +1,37 @@ +{ + "zarr_format": 3, + "node_type": "group", + "attributes": { + "ome": { + "version": "0.5", + "image-label": { + "colors": [ + { + "label-value": 0, + "rgba": [0, 0, 128, 128] + }, + { + "label-value": 1, + "rgba": [0, 128, 0, 128] + } + ], + "properties": [ + { + "label-value": 0, + "area (pixels)": 1200, + "class": "intercellular space" + }, + { + "label-value": 1, + "area (pixels)": 1650, + "class": "cell", + "cell type": "neuron" + } + ], + "source": { + "image": "../../" + } + } + } + } +} diff --git a/latest/examples/multiscales_strict/.config.json b/latest/examples/multiscales_strict/.config.json new file mode 100644 index 00000000..b0469538 --- /dev/null +++ b/latest/examples/multiscales_strict/.config.json @@ -0,0 +1,3 @@ +{ + "schema": "schemas/strict_image.schema" +} diff --git a/latest/examples/multiscales_strict/multiscales_example.json b/latest/examples/multiscales_strict/multiscales_example.json new file mode 100644 index 00000000..4b2c718a --- /dev/null +++ b/latest/examples/multiscales_strict/multiscales_example.json @@ -0,0 +1,68 @@ +{ + "zarr_format": 3, + "node_type": "group", + "attributes": { + "ome": { + "version": "0.5", + "multiscales": [ + { + "name": "example", + "axes": [ + { "name": "t", "type": "time", "unit": "millisecond" }, + { "name": "c", "type": "channel" }, + { "name": "z", "type": "space", "unit": "micrometer" }, + { "name": "y", "type": "space", "unit": "micrometer" }, + { "name": "x", "type": "space", "unit": "micrometer" } + ], + "datasets": [ + { + "path": "0", + "coordinateTransformations": [ + { + // the voxel size for the first scale level (0.5 micrometer) + "type": "scale", + "scale": [1.0, 1.0, 0.5, 0.5, 0.5] + } + ] + }, + { + "path": "1", + "coordinateTransformations": [ + { + // the voxel size for the second scale level (downscaled by a factor of 2 -> 1 micrometer) + "type": "scale", + "scale": [1.0, 1.0, 1.0, 1.0, 1.0] + } + ] + }, + { + "path": "2", + "coordinateTransformations": [ + { + // the voxel size for the third scale level (downscaled by a factor of 4 -> 2 micrometer) + "type": "scale", + "scale": [1.0, 1.0, 2.0, 2.0, 2.0] + } + ] + } + ], + "coordinateTransformations": [ + { + // the time unit (0.1 milliseconds), which is the same for each scale level + "type": "scale", + "scale": [0.1, 1.0, 1.0, 1.0, 1.0] + } + ], + "type": "gaussian", + "metadata": { + "description": "the fields in metadata depend on the downscaling implementation. Here, the parameters passed to the skimage function are given", + "method": "skimage.transform.pyramid_gaussian", + "version": "0.16.1", + "args": "[true]", + "kwargs": { "multichannel": true } + } + } + ] + } + } +} diff --git a/latest/examples/multiscales_strict/multiscales_transformations.json b/latest/examples/multiscales_strict/multiscales_transformations.json new file mode 100644 index 00000000..e4eb742a --- /dev/null +++ b/latest/examples/multiscales_strict/multiscales_transformations.json @@ -0,0 +1,47 @@ +{ + "zarr_format": 3, + "node_type": "group", + "attributes": { + "ome": { + "version": "0.5", + "multiscales": [ + { + "axes": [ + { + "name": "y", + "type": "space", + "unit": "micrometer" + }, + { + "name": "x", + "type": "space", + "unit": "micrometer" + } + ], + "datasets": [ + { + "path": "0", + "coordinateTransformations": [ + { + "scale": [1, 1], + "type": "scale" + } + ] + } + ], + "coordinateTransformations": [ + { + "scale": [10, 10], + "type": "scale" + } + ], + "name": "image_with_coordinateTransformations", + "type": "foo", + "metadata": { + "key": "value" + } + } + ] + } + } +} diff --git a/latest/examples/ome/.config.json b/latest/examples/ome/.config.json new file mode 100644 index 00000000..8a611ccf --- /dev/null +++ b/latest/examples/ome/.config.json @@ -0,0 +1,3 @@ +{ + "schema": "schemas/ome.schema" +} diff --git a/latest/examples/ome/series-2.json b/latest/examples/ome/series-2.json new file mode 100644 index 00000000..ad4c25e8 --- /dev/null +++ b/latest/examples/ome/series-2.json @@ -0,0 +1,10 @@ +{ + "zarr_format": 3, + "node_type": "group", + "attributes": { + "ome": { + "version": "0.5", + "series": ["0", "1"] + } + } +} diff --git a/latest/examples/plate_strict/.config.json b/latest/examples/plate_strict/.config.json new file mode 100644 index 00000000..a49b1743 --- /dev/null +++ b/latest/examples/plate_strict/.config.json @@ -0,0 +1,3 @@ +{ + "schema": "schemas/strict_plate.schema" +} diff --git a/latest/examples/plate_strict/plate_2wells.json b/latest/examples/plate_strict/plate_2wells.json new file mode 100644 index 00000000..e8961001 --- /dev/null +++ b/latest/examples/plate_strict/plate_2wells.json @@ -0,0 +1,97 @@ +{ + "zarr_format": 3, + "node_type": "group", + "attributes": { + "ome": { + "version": "0.5", + "plate": { + "acquisitions": [ + { + "id": 1, + "maximumfieldcount": 1, + "name": "single acquisition", + "starttime": 1343731272000 + } + ], + "columns": [ + { + "name": "1" + }, + { + "name": "2" + }, + { + "name": "3" + }, + { + "name": "4" + }, + { + "name": "5" + }, + { + "name": "6" + }, + { + "name": "7" + }, + { + "name": "8" + }, + { + "name": "9" + }, + { + "name": "10" + }, + { + "name": "11" + }, + { + "name": "12" + } + ], + "field_count": 1, + "name": "sparse test", + "rows": [ + { + "name": "A" + }, + { + "name": "B" + }, + { + "name": "C" + }, + { + "name": "D" + }, + { + "name": "E" + }, + { + "name": "F" + }, + { + "name": "G" + }, + { + "name": "H" + } + ], + "wells": [ + { + "path": "C/5", + "rowIndex": 2, + "columnIndex": 4 + }, + { + "path": "D/7", + "rowIndex": 3, + "columnIndex": 6 + } + ] + } + } + } +} diff --git a/latest/examples/plate_strict/plate_6wells.json b/latest/examples/plate_strict/plate_6wells.json new file mode 100644 index 00000000..bf1b8afe --- /dev/null +++ b/latest/examples/plate_strict/plate_6wells.json @@ -0,0 +1,78 @@ +{ + "zarr_format": 3, + "node_type": "group", + "attributes": { + "ome": { + "version": "0.5", + "plate": { + "acquisitions": [ + { + "id": 1, + "maximumfieldcount": 2, + "name": "Meas_01(2012-07-31_10-41-12)", + "starttime": 1343731272000 + }, + { + "id": 2, + "maximumfieldcount": 2, + "name": "Meas_02(201207-31_11-56-41)", + "starttime": 1343735801000 + } + ], + "columns": [ + { + "name": "1" + }, + { + "name": "2" + }, + { + "name": "3" + } + ], + "field_count": 4, + "name": "test", + "rows": [ + { + "name": "A" + }, + { + "name": "B" + } + ], + "wells": [ + { + "path": "A/1", + "rowIndex": 0, + "columnIndex": 0 + }, + { + "path": "A/2", + "rowIndex": 0, + "columnIndex": 1 + }, + { + "path": "A/3", + "rowIndex": 0, + "columnIndex": 2 + }, + { + "path": "B/1", + "rowIndex": 1, + "columnIndex": 0 + }, + { + "path": "B/2", + "rowIndex": 1, + "columnIndex": 1 + }, + { + "path": "B/3", + "rowIndex": 1, + "columnIndex": 2 + } + ] + } + } + } +} diff --git a/latest/examples/well_strict/.config.json b/latest/examples/well_strict/.config.json new file mode 100644 index 00000000..129ac69c --- /dev/null +++ b/latest/examples/well_strict/.config.json @@ -0,0 +1,3 @@ +{ + "schema": "schemas/strict_well.schema" +} diff --git a/latest/examples/well_strict/well_2fields.json b/latest/examples/well_strict/well_2fields.json new file mode 100644 index 00000000..987fe5e4 --- /dev/null +++ b/latest/examples/well_strict/well_2fields.json @@ -0,0 +1,21 @@ +{ + "zarr_format": 3, + "node_type": "group", + "attributes": { + "ome": { + "version": "0.5", + "well": { + "images": [ + { + "acquisition": 0, + "path": "0" + }, + { + "acquisition": 3, + "path": "1" + } + ] + } + } + } +} diff --git a/latest/examples/well_strict/well_4fields.json b/latest/examples/well_strict/well_4fields.json new file mode 100644 index 00000000..581ec66b --- /dev/null +++ b/latest/examples/well_strict/well_4fields.json @@ -0,0 +1,29 @@ +{ + "zarr_format": 3, + "node_type": "group", + "attributes": { + "ome": { + "version": "0.5", + "well": { + "images": [ + { + "acquisition": 1, + "path": "0" + }, + { + "acquisition": 1, + "path": "1" + }, + { + "acquisition": 2, + "path": "2" + }, + { + "acquisition": 2, + "path": "3" + } + ] + } + } + } +} diff --git a/latest/header.include b/latest/header.include new file mode 100644 index 00000000..e98bf6fe --- /dev/null +++ b/latest/header.include @@ -0,0 +1,34 @@ + + + + + + [TITLE] + + + +
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[TITLE]

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diff --git a/latest/index.bs b/latest/index.bs new file mode 100644 index 00000000..474119e3 --- /dev/null +++ b/latest/index.bs @@ -0,0 +1,718 @@ +
+Title: OME-Zarr specification
+Shortname: ome-zarr
+Level: 1
+Status: w3c/CG-FINAL
+TR: https://ngff.openmicroscopy.org/0.5/
+URL: https://ngff.openmicroscopy.org/0.5/
+Repository: https://github.com/ome/ngff
+Issue Tracking: Forums https://forum.image.sc/tag/ome-ngff
+Logo: http://www.openmicroscopy.org/img/logos/ome-logomark.svg
+Local Boilerplate: header yes, copyright yes
+Boilerplate: style-darkmode off
+Markup Shorthands: markdown yes
+Editor: Josh Moore, German BioImaging e.V., https://gerbi-gmb.de/, https://orcid.org/0000-0003-4028-811X
+Text Macro: NGFFVERSION 0.5
+Abstract: This document contains next-generation file format (NGFF)
+Abstract: specifications for storing bioimaging data in the cloud.
+Abstract: All specifications are submitted to the https://image.sc community for review.
+Status Text: The current released version of this specification is 0.5. Migration scripts
+Status Text: will be provided between numbered versions. Data written with these latest changes
+Status Text: (an "editor's draft") will not necessarily be supported.
+
+ +OME-Zarr specification {#ome-zarr} +---------------------------------- + +The conventions and specifications defined in this document are designed to +enable next-generation file formats to represent the same bioimaging data +that can be represented in \[OME-TIFF](http://www.openmicroscopy.org/ome-files/) +and beyond. + +Document conventions +-------------------- + +The key words “MUST”, “MUST NOT”, “REQUIRED”, “SHALL”, “SHALL NOT”, “SHOULD”, “SHOULD NOT”, +“RECOMMENDED”, “MAY”, and “OPTIONAL” are to be interpreted as described in +[RFC 2119](https://tools.ietf.org/html/rfc2119). + +

+Transitional metadata is added to the specification with the +intention of removing it in the future. Implementations may be expected (MUST) or +encouraged (SHOULD) to support the reading of the data, but writing will usually +be optional (MAY). Examples of transitional metadata include custom additions by +implementations that are later submitted as a formal specification. (See [[#bf2raw]]) +

+ +Some of the JSON examples in this document include comments. However, these are only for +clarity purposes and comments MUST NOT be included in JSON objects. + +Storage format {#storage-format} +================================ + +OME-Zarr is implemented using the Zarr format as defined by the +[version 3 of the Zarr specification](https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html). +All features of the Zarr format including codecs, chunk grids, chunk +key encodings, data types and storage transformers may be used with +OME-Zarr unless explicitly disallowed in this specification. + +An overview of the layout of an OME-Zarr fileset should make +understanding the following metadata sections easier. The hierarchy +is represented here as it would appear locally but could equally +be stored on a web server to be accessed via HTTP or in object storage +like S3 or GCS. + +Images {#image-layout} +---------------------- + +The following layout describes the expected Zarr hierarchy for images with +multiple levels of resolutions and optionally associated labels. +Note that the number of dimensions is variable between 2 and 5 and that axis names are arbitrary, see [[#multiscale-md]] for details. + +
+├── 123.zarr                  # One OME-Zarr image (id=123).
+│   ...
+│
+└── 456.zarr                  # Another OME-Zarr image (id=456).
+    │
+    ├── zarr.json             # Each image is a Zarr group of other groups and arrays.
+    │                         # Group level attributes are stored in the `zarr.json` file and include
+    │                         # "multiscales" and "omero" (see below).
+    │
+    ├── 0                     # Each multiscale level is stored as a separate Zarr array,
+    │   ...                   # which is a folder containing chunk files which compose the array.
+    ├── n                     # The name of the array is arbitrary with the ordering defined by
+    │   │                     # by the "multiscales" metadata, but is often a sequence starting at 0.
+    │   │
+    │   ├── zarr.json         # All image arrays must be up to 5-dimensional
+    │   │                     # with the axis of type time before type channel, before spatial axes.
+    │   │
+    │   └─ ...                # Chunks are stored conforming to the Zarr array specification and 
+    │                         # metadata as specified in the array's `zarr.json`.
+    │
+    └── labels
+        │
+        ├── zarr.json         # The labels group is a container which holds a list of labels to make the objects easily discoverable
+        │                     # All labels will be listed in `zarr.json` e.g. `{ "labels": [ "original/0" ] }`
+        │                     # Each dimension of the label should be either the same as the
+        │                     # corresponding dimension of the image, or `1` if that dimension of the label
+        │                     # is irrelevant.
+        │
+        └── original          # Intermediate folders are permitted but not necessary and currently contain no extra metadata.
+            │
+            └── 0             # Multiscale, labeled image. The name is unimportant but is registered in the "labels" group above.
+                ├── zarr.json # Zarr Group which is both a multiscaled image as well as a labeled image.
+                │             # Metadata of the related image and as well as display information under the "image-label" key.
+                │
+                ├── 0         # Each multiscale level is stored as a separate Zarr array, as above, but only integer values
+                └── ...       # are supported.
+                
+
+ + + +High-content screening {#hcs-layout} +------------------------------------ + +The following specification defines the hierarchy for a high-content screening +dataset. Three groups MUST be defined above the images: + +- the group above the images defines the well and MUST implement the + [well specification](#well-md). All images contained in a well are fields + of view of the same well +- the group above the well defines a row of wells +- the group above the well row defines an entire plate i.e. a two-dimensional + collection of wells organized in rows and columns. It MUST implement the + [plate specification](#plate-md) + +A well row group SHOULD NOT be present if there are no images in the well row. +A well group SHOULD NOT be present if there are no images in the well. + + +
+.
+│
+└── 5966.zarr                 # One OME-Zarr plate (id=5966)
+    ├── zarr.json             # Implements "plate" specification
+    ├── A                     # First row of the plate
+    │   ├── zarr.json
+    │   │
+    │   ├── 1                 # First column of row A
+    │   │   ├── zarr.json     # Implements "well" specification
+    │   │   │
+    │   │   ├── 0             # First field of view of well A1
+    │   │   │   │
+    │   │   │   ├── zarr.json # Implements "multiscales", "omero"
+    │   │   │   ├── 0         # Resolution levels          
+    │   │   │   ├── ...
+    │   │   │   └── labels    # Labels (optional)
+    │   │   └── ...           # Other fields of view
+    │   └── ...               # Other columns
+    └── ...                   # Other rows
+
+ +OME-Zarr Metadata {#metadata} +============================= + +The "OME-Zarr Metadata" contains metadata keys as specified below +for discovering certain types of data, especially images. + +The OME-Zarr Metadata is stored in the various `zarr.json` files throughout the above array +hierarchy. In this file, the metadata is stored under the namespaced key +`ome` in `attributes`. +The version of the OME-Zarr Metadata is denoted as a string in the `version` attribute within the `ome` namespace. + +The OME-Zarr Metadata version MUST be consistent within a hierarchy. + +```json +{ + ... + "attributes": { + "ome": { + "version": "0.5", + ... + } + } +} +``` + +"axes" metadata {#axes-md} +-------------------------- + +"axes" describes the dimensions of a physical coordinate space. It is a list of dictionaries, where each dictionary describes a dimension (axis) and: +- MUST contain the field "name" that gives the name for this dimension. The values MUST be unique across all "name" fields. +- SHOULD contain the field "type". It SHOULD be one of "space", "time" or "channel", but MAY take other string values for custom axis types that are not part of this specification yet. +- SHOULD contain the field "unit" to specify the physical unit of this dimension. The value SHOULD be one of the following strings, which are valid units according to UDUNITS-2. + - Units for "space" axes: 'angstrom', 'attometer', 'centimeter', 'decimeter', 'exameter', 'femtometer', 'foot', 'gigameter', 'hectometer', 'inch', 'kilometer', 'megameter', 'meter', 'micrometer', 'mile', 'millimeter', 'nanometer', 'parsec', 'petameter', 'picometer', 'terameter', 'yard', 'yoctometer', 'yottameter', 'zeptometer', 'zettameter' + - Units for "time" axes: 'attosecond', 'centisecond', 'day', 'decisecond', 'exasecond', 'femtosecond', 'gigasecond', 'hectosecond', 'hour', 'kilosecond', 'megasecond', 'microsecond', 'millisecond', 'minute', 'nanosecond', 'petasecond', 'picosecond', 'second', 'terasecond', 'yoctosecond', 'yottasecond', 'zeptosecond', 'zettasecond' + +The "axes" are used as part of [[#multiscale-md]]. The length of "axes" MUST be equal to the number of dimensions of the arrays that contain the image data. + +The "dimension_names" attribute in the `zarr.json` of the Zarr array of a multiscale level MUST match the names in the "axes" metadata. + + +"bioformats2raw.layout" (transitional) {#bf2raw} +------------------------------------------------ + +[=Transitional=] "bioformats2raw.layout" metadata identifies a group which implicitly describes a series of images. +The need for the collection stems from the common "multi-image file" scenario in microscopy. Parsers like Bio-Formats +define a strict, stable ordering of the images in a single container that can be used to refer to them by other tools. + +In order to capture that information within an OME-Zarr dataset, `bioformats2raw` internally introduced a wrapping layer. +The bioformats2raw layout has been added to v0.4 as a transitional specification to specify filesets that already exist +in the wild. An upcoming NGFF specification will replace this layout with explicit metadata. + +

Layout

+ +Typical Zarr layout produced by running `bioformats2raw` on a fileset that contains more than one image (series > 1): + +
+series.ome.zarr               # One converted fileset from bioformats2raw
+    ├── zarr.json             # Contains "bioformats2raw.layout" metadata
+    ├── OME                   # Special group for containing OME metadata
+    │   ├── zarr.json         # Contains "series" metadata
+    │   └── METADATA.ome.xml  # OME-XML file stored within the Zarr fileset
+    ├── 0                     # First image in the collection
+    ├── 1                     # Second image in the collection
+    └── ...
+
+ +

Attributes

+ +The OME-Zarr Metadata in the top-level `zarr.json` file must contain the `bioformats2raw.layout` key: +
+path: examples/bf2raw/image.json
+highlight: json
+
+ +If the top-level group represents a plate, the `bioformats2raw.layout` metadata will be present but +the "plate" key MUST also be present, takes precedence and parsing of such datasets should follow [[#plate-md]]. It is not +possible to mix collections of images with plates at present. + +
+path: examples/bf2raw/plate.json
+highlight: json
+
+ +The OME-Zarr Metadata in the `zarr.json` file within the OME group may contain the "series" key: + +
+path: examples/ome/series-2.json
+highlight: json
+
+ +

Details

+ +Conforming groups: + +- MUST have the value "3" for the "bioformats2raw.layout" key in their OME-Zarr Metadata in the `zarr.json` at the top of the hierarchy; +- SHOULD have OME metadata representing the entire collection of images in a file named "OME/METADATA.ome.xml" which: + - MUST adhere to the OME-XML specification but + - MUST use `` elements as opposed to ``, `` or ``; + - MAY make use of the [minimum specification](https://docs.openmicroscopy.org/ome-model/6.2.2/specifications/minimum.html). + +Additionally, the logic for finding the Zarr group for each image follows the following logic: + +- If "plate" metadata is present, images MUST be located at the defined location. + - Matching "series" metadata (as described next) SHOULD be provided for tools that are unaware of the "plate" specification. +- If the "OME" Zarr group exists, it: + - MAY contain a "series" attribute. If so: + - "series" MUST be a list of string objects, each of which is a path to an image group. + - The order of the paths MUST match the order of the "Image" elements in "OME/METADATA.ome.xml" if provided. +- If the "series" attribute does not exist and no "plate" is present: + - separate "multiscales" images MUST be stored in consecutively numbered groups starting from 0 (i.e. "0/", "1/", "2/", "3/", ...). +- Every "multiscales" group MUST represent exactly one OME-XML "Image" in the same order as either the series index or the group numbers. + +Conforming readers: +- SHOULD make users aware of the presence of more than one image (i.e. SHOULD NOT default to only opening the first image); +- MAY use the "series" attribute in the "OME" group to determine a list of valid groups to display; +- MAY choose to show all images within the collection or offer the user a choice of images, as with HCS plates; +- MAY ignore other groups or arrays under the root of the hierarchy. + + +"coordinateTransformations" metadata {#trafo-md} +------------------------------------------------ + +"coordinateTransformations" describe a series of transformations that map between two coordinate spaces (defined by "axes"). +For example, to map a discrete data space of an array to the corresponding physical space. +It is a list of dictionaries. Each entry describes a single transformation and MUST contain the field "type". +The value of "type" MUST be one of the elements of the `type` column in the table below. +Additional fields for the entry depend on "type" and are defined by the column `fields`. + + + +
`identity` identity transformation, is the default transformation and is typically not explicitly defined +
`translation` one of: `"translation":List[float]`, `"path":str` translation vector, stored either as a list of floats (`"translation"`) or as binary data at a location in this container (`path`). The length of vector defines number of dimensions. | +
`scale` one of: `"scale":List[float]`, `"path":str` scale vector, stored either as a list of floats (`scale`) or as binary data at a location in this container (`path`). The length of vector defines number of dimensions. | +
typefieldsdescription +
+ +The transformations in the list are applied sequentially and in order. + + +"multiscales" metadata {#multiscale-md} +--------------------------------------- + +Metadata about an image can be found under the "multiscales" key in the group-level OME-Zarr Metadata. +Here, image refers to 2 to 5 dimensional data representing image or volumetric data with optional time or channel axes. +It is stored in a multiple resolution representation. + +"multiscales" contains a list of dictionaries where each entry describes a multiscale image. + +Each "multiscales" dictionary MUST contain the field "axes", see [[#axes-md]]. +The length of "axes" must be between 2 and 5 and MUST be equal to the dimensionality of the zarr arrays storing the image data (see "datasets:path"). +The "axes" MUST contain 2 or 3 entries of "type:space" and MAY contain one additional entry of "type:time" and MAY contain one additional entry of "type:channel" or a null / custom type. +The order of the entries MUST correspond to the order of dimensions of the zarr arrays. In addition, the entries MUST be ordered by "type" where the "time" axis must come first (if present), followed by the "channel" or custom axis (if present) and the axes of type "space". +If there are three spatial axes where two correspond to the image plane ("yx") and images are stacked along the other (anisotropic) axis ("z"), the spatial axes SHOULD be ordered as "zyx". + +Each "multiscales" dictionary MUST contain the field "datasets", which is a list of dictionaries describing the arrays storing the individual resolution levels. +Each dictionary in "datasets" MUST contain the field "path", whose value contains the path to the array for this resolution relative +to the current zarr group. The "path"s MUST be ordered from largest (i.e. highest resolution) to smallest. + +Each "datasets" dictionary MUST have the same number of dimensions and MUST NOT have more than 5 dimensions. The number of dimensions and order MUST correspond to number and order of "axes". +Each dictionary in "datasets" MUST contain the field "coordinateTransformations", which contains a list of transformations that map the data coordinates to the physical coordinates (as specified by "axes") for this resolution level. +The transformations are defined according to [[#trafo-md]]. The transformation MUST only be of type `translation` or `scale`. +They MUST contain exactly one `scale` transformation that specifies the pixel size in physical units or time duration. If scaling information is not available or applicable for one of the axes, the value MUST express the scaling factor between the current resolution and the first resolution for the given axis, defaulting to 1.0 if there is no downsampling along the axis. +It MAY contain exactly one `translation` that specifies the offset from the origin in physical units. If `translation` is given it MUST be listed after `scale` to ensure that it is given in physical coordinates. +The length of the `scale` and `translation` array MUST be the same as the length of "axes". +The requirements (only `scale` and `translation`, restrictions on order) are in place to provide a simple mapping from data coordinates to physical coordinates while being compatible with the general transformation spec. + +Each "multiscales" dictionary MAY contain the field "coordinateTransformations", describing transformations that are applied to all resolution levels in the same manner. +The transformations MUST follow the same rules about allowed types, order, etc. as in "datasets:coordinateTransformations" and are applied after them. +They can for example be used to specify the `scale` for a dimension that is the same for all resolutions. + +Each "multiscales" dictionary SHOULD contain the field "name". + +Each "multiscales" dictionary SHOULD contain the field "type", which gives the type of downscaling method used to generate the multiscale image pyramid. +It SHOULD contain the field "metadata", which contains a dictionary with additional information about the downscaling method. + +
+path: examples/multiscales_strict/multiscales_example.json
+highlight: json
+
+ + +If only one multiscale is provided, use it. Otherwise, the user can choose by +name, using the first multiscale as a fallback: + +```python +datasets = [] +for named in multiscales: + if named["name"] == "3D": + datasets = [x["path"] for x in named["datasets"]] + break +if not datasets: + # Use the first by default. Or perhaps choose based on chunk size. + datasets = [x["path"] for x in multiscales[0]["datasets"]] +``` + +"omero" metadata (transitional) {#omero-md} +------------------------------------------- + +[=Transitional=] information specific to the channels of an image and how to render it +can be found under the "omero" key in the group-level metadata: + +```json +"id": 1, # ID in OMERO +"name": "example.tif", # Name as shown in the UI +"channels": [ # Array matching the c dimension size + { + "active": true, + "coefficient": 1, + "color": "0000FF", + "family": "linear", + "inverted": false, + "label": "LaminB1", + "window": { + "end": 1500, + "max": 65535, + "min": 0, + "start": 0 + } + } +], +"rdefs": { + "defaultT": 0, # First timepoint to show the user + "defaultZ": 118, # First Z section to show the user + "model": "color" # "color" or "greyscale" +} +``` + +See the [OMERO WebGateway documentation](https://omero.readthedocs.io/en/stable/developers/Web/WebGateway.html#imgdata) +for more information. + +"labels" metadata {#labels-md} +------------------------------ + +In OME-Zarr, Zarr arrays representing pixel-annotation data are stored in a group called "labels". Some applications--notably image segmentation--produce +a new image that is in the same coordinate system as a corresponding multiscale image (usually having the same dimensions and coordinate transformations). +This new image is composed of integer values corresponding to certain labels with custom meanings. For example, pixels take the value 1 or 0 +if the corresponding pixel in the original image represents cellular space or intercellular space, respectively. +Such an image is referred to in this specification as a 'label image'. + +The "labels" group is nested within an image group, at the same level of the Zarr hierarchy as the resolution levels for the original image. +The "labels" group is not itself an image; it contains images. The pixels of the label images MUST be integer data types, i.e. one of +[`uint8`, `int8`, `uint16`, `int16`, `uint32`, `int32`, `uint64`, `int64`]. Intermediate groups between "labels" and the images within it are allowed, +but these MUST NOT contain metadata. Names of the images in the "labels" group are arbitrary. + +The OME-Zarr Metadata in the `zarr.json` file associated with the "labels" group MUST contain a JSON object with the key `labels`, whose value is a JSON array of paths to the +labeled multiscale image(s). All label images SHOULD be listed within this metadata file. For example: + +```json +{ + ... + "attributes": { + "ome": { + "version": "0.5", + "labels": [ + "cell_space_segmentation" + ] + } + } +} +``` + +The `zarr.json` file for the label image MUST implement the multiscales specification. Within the `multiscales` object, the JSON array +associated with the `datasets` key MUST have the same number of entries (scale levels) as the original unlabeled image. + +In addition to the `multiscales` key, the OME-Zarr Metadata in this image-level `zarr.json` file SHOULD contain another key, `image-label`, +whose value is also a JSON object. The `image-label` object stores information about the display colors, source image, and optionally, +further arbitrary properties of the label image. That `image-label` object SHOULD contain the following keys: first, a `colors` key, +whose value MUST be a JSON array describing color information for the unique label values. Second, a `version` key, whose value MUST be a +string specifying the version of the OME-Zarr `image-label` schema. + +Conforming readers SHOULD display labels using the colors specified by the `colors` JSON array, as follows. This array contains one +JSON object for each unique custom label. Each of these objects MUST contain the `label-value` key, whose value MUST be the integer +corresponding to a particular label. In addition to the `label-value` key, the objects in this array MAY contain an `rgba` key whose +value MUST be an array of four integers between 0 and 255, inclusive. These integers represent the `uint8` values of red, green, and +blue that comprise the final color to be displayed at the pixels with this label. The fourth integer in the `rgba` array represents alpha, +or the opacity of the color. Additional keys under `colors` are allowed. + +Next, the `image-label` object MAY contain the following keys: a `properties` key, and a `source` key. + +Like the `colors` key, the value of the `properties` key MUST be an array of JSON objects describing the set of unique possible pixel values. +Each object in the `properties` array MUST contain the `label-value` key, whose value again MUST be an integer specifying the pixel value for that label. +Additionally, an arbitrary number of key-value pairs MAY be present for each label value, denoting arbitrary metadata associated with that label. +Label-value objects within the `properties` array do not need to have the same keys. + +The value of the `source` key MUST be a JSON object containing information about the original image from which the label image derives. +This object MAY include a key `image`, whose value MUST be a string specifying the relative path to a Zarr image group. +The default value is `../../` since most labeled images are stored in a "labels" group that is nested within the original image group. + +Here is an example of a simple `image-label` object for a label image in which 0s and 1s represent intercellular and cellular space, respectively: + +
+path: examples/label_strict/colors_properties.json
+highlight: json
+
+ +In this case, the pixels consisting of a 0 in the Zarr array will be displayed as 50% blue and 50% opacity. Pixels with a 1 in the Zarr array, +which correspond to cellular space, will be displayed as 50% green and 50% opacity. + +"plate" metadata {#plate-md} +---------------------------- + +For high-content screening datasets, the plate layout can be found under the +custom attributes of the plate group under the `plate` key in the group-level metadata. + +The `plate` dictionary MAY contain an `acquisitions` key whose value MUST be a list of +JSON objects defining the acquisitions for a given plate to which wells can refer to. Each +acquisition object MUST contain an `id` key whose value MUST be an unique integer identifier +greater than or equal to 0 within the context of the plate to which fields of view can refer +to (see #well-md). +Each acquisition object SHOULD contain a `name` key whose value MUST be a string identifying +the name of the acquisition. Each acquisition object SHOULD contain a `maximumfieldcount` +key whose value MUST be a positive integer indicating the maximum number of fields of view for the +acquisition. Each acquisition object MAY contain a `description` key whose value MUST be a +string specifying a description for the acquisition. Each acquisition object MAY contain +a `starttime` and/or `endtime` key whose values MUST be integer epoch timestamps specifying +the start and/or end timestamp of the acquisition. + +The `plate` dictionary MUST contain a `columns` key whose value MUST be a list of JSON objects +defining the columns of the plate. Each column object defines the properties of +the column at the index of the object in the list. Each column in the physical plate +MUST be defined, even if no wells in the column are defined. Each column object MUST +contain a `name` key whose value is a string specifying the column name. The `name` MUST +contain only alphanumeric characters, MUST be case-sensitive, and MUST NOT be a duplicate of any +other `name` in the `columns` list. Care SHOULD be taken to avoid collisions on +case-insensitive filesystems (e.g. avoid using both `Aa` and `aA`). + +The `plate` dictionary SHOULD contain a `field_count` key whose value MUST be a positive integer +defining the maximum number of fields per view across all wells. + +The `plate` dictionary SHOULD contain a `name` key whose value MUST be a string defining the +name of the plate. + +The `plate` dictionary MUST contain a `rows` key whose value MUST be a list of JSON objects +defining the rows of the plate. Each row object defines the properties of +the row at the index of the object in the list. Each row in the physical plate +MUST be defined, even if no wells in the row are defined. Each defined row MUST +contain a `name` key whose value MUST be a string defining the row name. The `name` MUST +contain only alphanumeric characters, MUST be case-sensitive, and MUST NOT be a duplicate of any +other `name` in the `rows` list. Care SHOULD be taken to avoid collisions on +case-insensitive filesystems (e.g. avoid using both `Aa` and `aA`). + +The `plate` dictionary MUST contain a `version` key whose value MUST be a string specifying the +version of the plate specification. + +The `plate` dictionary MUST contain a `wells` key whose value MUST be a list of JSON objects +defining the wells of the plate. Each well object MUST contain a `path` key whose value MUST +be a string specifying the path to the well subgroup. The `path` MUST consist of a `name` in +the `rows` list, a file separator (`/`), and a `name` from the `columns` list, in that order. +The `path` MUST NOT contain additional leading or trailing directories. +Each well object MUST contain both a `rowIndex` key whose value MUST be an integer identifying +the index into the `rows` list and a `columnIndex` key whose value MUST be an integer identifying +the index into the `columns` list. `rowIndex` and `columnIndex` MUST be 0-based. The +`rowIndex`, `columnIndex`, and `path` MUST all refer to the same row/column pair. + +For example the following JSON object defines a plate with two acquisitions and +6 wells (2 rows and 3 columns), containing up to 2 fields of view per acquisition. + +
+path: examples/plate_strict/plate_6wells.json
+highlight: json
+
+ +The following JSON object defines a sparse plate with one acquisition and +2 wells in a 96 well plate, containing one field of view per acquisition. + +
+path: examples/plate_strict/plate_2wells.json
+highlight: json
+
+ +"well" metadata {#well-md} +-------------------------- + +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. + +The `well` dictionary MUST contain an `images` key whose value MUST be a list of JSON objects +specifying all fields of views for a given well. Each image object MUST contain a +`path` key whose value MUST be a string specifying the path to the field of view. The `path` +MUST contain only alphanumeric characters, MUST be case-sensitive, and MUST NOT be a duplicate +of any other `path` in the `images` list. If multiple acquisitions were performed in the plate, +it MUST contain an `acquisition` key whose value MUST be an integer identifying the acquisition +which MUST match one of the acquisition JSON objects defined in the plate metadata (see #plate-md). + +The `well` dictionary SHOULD contain a `version` key whose value MUST be a string specifying the +version of the well specification. + +For example the following JSON object defines a well with four fields of +view. The first two fields of view were part of the first acquisition while +the last two fields of view were part of the second acquisition. + +
+path: examples/well_strict/well_4fields.json
+highlight: json
+
+ +The following JSON object defines a well with two fields of view in a plate with +four acquisitions. The first field is part of the first acquisition, and the second +field is part of the last acquisition. + +
+path: examples/well_strict/well_2fields.json
+highlight: json
+
+ +Specification naming style {#naming-style} +========================================== + +Multi-word keys in this specification should use the `camelCase` style. +NB: some parts of the specification don't obey this convention as they +were added before this was adopted, but they should be updated in due course. + +Implementations {#implementations} +================================== + +See [Tools](https://ngff.openmicroscopy.org/tools/index.html). + +Citing {#citing} +================ + +[Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.](https://ngff.openmicroscopy.org/0.4) +J. Moore, *et al*. Open Microscopy Environment Consortium, 8 February 2022. +This edition of the specification is [https://ngff.openmicroscopy.org/0.5/](https://ngff.openmicroscopy.org/0.5/]). +The latest edition is available at [https://ngff.openmicroscopy.org/latest/](https://ngff.openmicroscopy.org/latest/). +[(doi:10.5281/zenodo.4282107)](https://doi.org/10.5281/zenodo.4282107) + +Version History {#history} +========================== + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
RevisionDateDescription
0.52024-11-21use Zarr v3 in OME-Zarr, see RFC-2.
0.4.12023-02-09expand on "labels" description
0.4.12022-09-26transitional metadata for image collections ("bioformats2raw.layout")
0.4.02022-02-08multiscales: add axes type, units and coordinateTransformations
0.4.02022-02-08plate: add rowIndex/columnIndex
0.3.02021-08-24Add axes field to multiscale metadata
0.2.02021-03-29Change chunk dimension separator to "/"
0.1.42020-11-26Add HCS specification
0.1.32020-09-14Add labels specification
0.1.2 2020-05-07Add description of "omero" metadata
0.1.1 2020-05-06Add info on the ordering of resolutions
0.1.0 2020-04-20First version for internal demo
+ + +
+{
+  "blogNov2020": {
+    "href": "https://blog.openmicroscopy.org/file-formats/community/2020/11/04/zarr-data/",
+    "title": "Public OME-Zarr data (Nov. 2020)",
+    "authors": [
+      "OME Team"
+    ],
+    "status": "Informational",
+    "publisher": "OME",
+    "id": "blogNov2020",
+    "date": "04 November 2020"
+  },
+  "imagesc26952": {
+    "href": "https://forum.image.sc/t/ome-s-position-regarding-file-formats/26952",
+    "title": "OME’s position regarding file formats",
+    "authors": [
+      "OME Team"
+    ],
+    "status": "Informational",
+    "publisher": "OME",
+    "id": "imagesc26952",
+    "date": "19 June 2020"
+  },
+  "n5": {
+    "id": "n5",
+    "href": "https://github.com/saalfeldlab/n5/issues/62",
+    "title": "N5---a scalable Java API for hierarchies of chunked n-dimensional tensors and structured meta-data",
+    "status": "Informational",
+    "authors": [
+      "John A. Bogovic",
+      "Igor Pisarev",
+      "Philipp Hanslovsky",
+      "Neil Thistlethwaite",
+      "Stephan Saalfeld"
+    ],
+    "date": "2020"
+  },
+  "ome-zarr-py": {
+    "id": "ome-zarr-py",
+    "href": "https://doi.org/10.5281/zenodo.4113931",
+    "title": "ome-zarr-py: Experimental implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.",
+    "status": "Informational",
+    "publisher": "Zenodo",
+    "authors": [
+      "OME",
+      "et al"
+    ],
+    "date": "06 October 2020"
+  },
+  "zarr": {
+    "id": "zarr",
+    "href": "https://doi.org/10.5281/zenodo.4069231",
+    "title": "Zarr: An implementation of chunked, compressed, N-dimensional arrays for Python.",
+    "status": "Informational",
+    "publisher": "Zenodo",
+    "authors": [
+      "Alistair Miles",
+      "et al"
+    ],
+    "date": "06 October 2020"
+  }
+}
+
diff --git a/latest/schemas/_version.schema b/latest/schemas/_version.schema new file mode 100644 index 00000000..1da06a6d --- /dev/null +++ b/latest/schemas/_version.schema @@ -0,0 +1,10 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://ngff.openmicroscopy.org/0.5/schemas/_version.schema", + "title": "OME-Zarr Metadata version", + "description": "The version of the OME-Zarr Metadata", + "type": "string", + "enum": [ + "0.5" + ] +} diff --git a/latest/schemas/bf2raw.schema b/latest/schemas/bf2raw.schema new file mode 100644 index 00000000..d3c87253 --- /dev/null +++ b/latest/schemas/bf2raw.schema @@ -0,0 +1,32 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://ngff.openmicroscopy.org/0.5/schemas/bf2raw.schema", + "title": "OME-Zarr container produced by bioformats2raw", + "description": "The zarr.json attributes key", + "type": "object", + "properties": { + "ome": { + "description": "The versioned OME-Zarr Metadata namespace", + "type": "object", + "properties": { + "bioformats2raw.layout": { + "description": "The top-level identifier metadata added by bioformats2raw", + "type": "number", + "enum": [ + 3 + ] + }, + "version": { + "$ref": "https://ngff.openmicroscopy.org/0.5/schemas/_version.schema" + } + }, + "required": [ + "bioformats2raw.layout", + "version" + ] + } + }, + "required": [ + "ome" + ] +} diff --git a/latest/schemas/image.schema b/latest/schemas/image.schema new file mode 100644 index 00000000..f94fd942 --- /dev/null +++ b/latest/schemas/image.schema @@ -0,0 +1,268 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://ngff.openmicroscopy.org/0.5/schemas/image.schema", + "title": "OME-Zarr Image", + "description": "The zarr.json attributes key", + "type": "object", + "properties": { + "ome": { + "description": "The versioned OME-Zarr Metadata namespace", + "type": "object", + "properties": { + "multiscales": { + "$ref": "#/$defs/multiscales" + }, + "omero": { + "$ref": "#/$defs/omero" + }, + "version": { + "$ref": "https://ngff.openmicroscopy.org/0.5/schemas/_version.schema" + } + }, + "required": [ + "multiscales", + "version" + ] + } + }, + "required": [ + "ome" + ], + "$defs": { + "multiscales": { + "description": "The multiscale datasets for this image", + "type": "array", + "items": { + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "datasets": { + "type": "array", + "minItems": 1, + "items": { + "type": "object", + "properties": { + "path": { + "type": "string" + }, + "coordinateTransformations": { + "$ref": "#/$defs/coordinateTransformations" + } + }, + "required": [ + "path", + "coordinateTransformations" + ] + } + }, + "axes": { + "$ref": "#/$defs/axes" + }, + "coordinateTransformations": { + "$ref": "#/$defs/coordinateTransformations" + } + }, + "required": [ + "datasets", + "axes" + ] + }, + "minItems": 1, + "uniqueItems": true + }, + "omero": { + "type": "object", + "properties": { + "channels": { + "type": "array", + "items": { + "type": "object", + "properties": { + "window": { + "type": "object", + "properties": { + "end": { + "type": "number" + }, + "max": { + "type": "number" + }, + "min": { + "type": "number" + }, + "start": { + "type": "number" + } + }, + "required": [ + "start", + "min", + "end", + "max" + ] + }, + "label": { + "type": "string" + }, + "family": { + "type": "string" + }, + "color": { + "type": "string" + }, + "active": { + "type": "boolean" + } + } + } + } + }, + "required": [ + "channels" + ] + }, + "axes": { + "type": "array", + "uniqueItems": true, + "minItems": 2, + "maxItems": 5, + "contains": { + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "type": { + "type": "string", + "enum": [ + "space" + ] + }, + "unit": { + "type": "string" + } + } + }, + "minContains": 2, + "maxContains": 3, + "items": { + "oneOf": [ + { + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "type": { + "type": "string", + "enum": [ + "channel", + "time", + "space" + ] + } + }, + "required": [ + "name", + "type" + ] + }, + { + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "type": { + "type": "string", + "not": { + "enum": [ + "space", + "time", + "channel" + ] + } + } + }, + "required": [ + "name" + ] + } + ] + } + }, + "coordinateTransformations": { + "type": "array", + "minItems": 1, + "contains": { + "type": "object", + "properties": { + "type": { + "type": "string", + "enum": [ + "scale" + ] + }, + "scale": { + "type": "array", + "minItems": 2, + "items": { + "type": "number" + } + } + } + }, + "maxContains": 1, + "items": { + "oneOf": [ + { + "type": "object", + "properties": { + "type": { + "type": "string", + "enum": [ + "scale" + ] + }, + "scale": { + "type": "array", + "minItems": 2, + "items": { + "type": "number" + } + } + }, + "required": [ + "type", + "scale" + ] + }, + { + "type": "object", + "properties": { + "type": { + "type": "string", + "enum": [ + "translation" + ] + }, + "translation": { + "type": "array", + "minItems": 2, + "items": { + "type": "number" + } + } + }, + "required": [ + "type", + "translation" + ] + } + ] + } + } + } +} diff --git a/latest/schemas/label.schema b/latest/schemas/label.schema new file mode 100644 index 00000000..dd5cb6d6 --- /dev/null +++ b/latest/schemas/label.schema @@ -0,0 +1,91 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://ngff.openmicroscopy.org/0.5/schemas/label.schema", + "title": "OME-Zarr labelled image schema", + "description": "The zarr.json attributes key", + "type": "object", + "properties": { + "ome": { + "description": "The versioned OME-Zarr Metadata namespace", + "type": "object", + "properties": { + "image-label": { + "$ref": "#/$defs/image-label" + }, + "version": { + "$ref": "https://ngff.openmicroscopy.org/0.5/schemas/_version.schema" + } + }, + "required": [ + "image-label", + "version" + ] + } + }, + "required": [ + "ome" + ], + "$defs": { + "image-label": { + "type": "object", + "properties": { + "colors": { + "description": "The colors for this label image", + "type": "array", + "items": { + "type": "object", + "properties": { + "label-value": { + "description": "The value of the label", + "type": "number" + }, + "rgba": { + "description": "The RGBA color stored as an array of four integers between 0 and 255", + "type": "array", + "items": { + "type": "integer", + "minimum": 0, + "maximum": 255 + }, + "minItems": 4, + "maxItems": 4 + } + }, + "required": [ + "label-value" + ] + }, + "minItems": 1, + "uniqueItems": true + }, + "properties": { + "description": "The properties for this label image", + "type": "array", + "items": { + "type": "object", + "properties": { + "label-value": { + "description": "The pixel value for this label", + "type": "integer" + } + }, + "required": [ + "label-value" + ] + }, + "minItems": 1, + "uniqueItems": true + }, + "source": { + "description": "The source of this label image", + "type": "object", + "properties": { + "image": { + "type": "string" + } + } + } + } + } + } +} diff --git a/latest/schemas/ome.schema b/latest/schemas/ome.schema new file mode 100644 index 00000000..36569280 --- /dev/null +++ b/latest/schemas/ome.schema @@ -0,0 +1,33 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://ngff.openmicroscopy.org/0.5/schemas/ome.schema", + "title": "OME-Zarr group produced by bioformats2raw to contain OME metadata", + "description": "The zarr.json attributes key", + "type": "object", + "properties": { + "ome": { + "description": "The versioned OME-Zarr Metadata namespace", + "type": "object", + "properties": { + "series": { + "description": "An array of the same length and the same order as the images defined in the OME-XML", + "type": "array", + "items": { + "type": "string" + }, + "minContains": 1 + }, + "version": { + "$ref": "https://ngff.openmicroscopy.org/0.5/schemas/_version.schema" + } + }, + "required": [ + "series", + "version" + ] + } + }, + "required": [ + "ome" + ] +} diff --git a/latest/schemas/ome_zarr.schema b/latest/schemas/ome_zarr.schema new file mode 100644 index 00000000..9b22bba6 --- /dev/null +++ b/latest/schemas/ome_zarr.schema @@ -0,0 +1,24 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://ngff.openmicroscopy.org/0.5/schemas/ome_zarr.schema", + "anyOf": [ + { + "$ref": "https://ngff.openmicroscopy.org/0.5/schemas/bf2raw.schema" + }, + { + "$ref": "https://ngff.openmicroscopy.org/0.5/schemas/image.schema" + }, + { + "$ref": "https://ngff.openmicroscopy.org/0.5/schemas/label.schema" + }, + { + "$ref": "https://ngff.openmicroscopy.org/0.5/schemas/ome.schema" + }, + { + "$ref": "https://ngff.openmicroscopy.org/0.5/schemas/plate.schema" + }, + { + "$ref": "https://ngff.openmicroscopy.org/0.5/schemas/well.schema" + } + ] +} diff --git a/latest/schemas/plate.schema b/latest/schemas/plate.schema new file mode 100644 index 00000000..3c8a1b97 --- /dev/null +++ b/latest/schemas/plate.schema @@ -0,0 +1,153 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://ngff.openmicroscopy.org/0.5/schemas/plate.schema", + "title": "OME-Zarr plate schema", + "description": "The zarr.json attributes key", + "type": "object", + "properties": { + "ome": { + "description": "The versioned OME-Zarr Metadata namespace", + "type": "object", + "properties": { + "plate": { + "type": "object", + "properties": { + "acquisitions": { + "description": "The acquisitions for this plate", + "type": "array", + "items": { + "type": "object", + "properties": { + "id": { + "description": "A unique identifier within the context of the plate", + "type": "integer", + "minimum": 0 + }, + "maximumfieldcount": { + "description": "The maximum number of fields of view for the acquisition", + "type": "integer", + "exclusiveMinimum": 0 + }, + "name": { + "description": "The name of the acquisition", + "type": "string" + }, + "description": { + "description": "The description of the acquisition", + "type": "string" + }, + "starttime": { + "description": "The start timestamp of the acquisition, expressed as epoch time i.e. the number seconds since the Epoch", + "type": "integer", + "minimum": 0 + }, + "endtime": { + "description": "The end timestamp of the acquisition, expressed as epoch time i.e. the number seconds since the Epoch", + "type": "integer", + "minimum": 0 + } + }, + "required": [ + "id" + ] + } + }, + "field_count": { + "description": "The maximum number of fields per view across all wells", + "type": "integer", + "exclusiveMinimum": 0 + }, + "name": { + "description": "The name of the plate", + "type": "string" + }, + "columns": { + "description": "The columns of the plate", + "type": "array", + "items": { + "type": "object", + "properties": { + "name": { + "description": "The column name", + "type": "string", + "pattern": "^[A-Za-z0-9]+$" + } + }, + "required": [ + "name" + ] + }, + "minItems": 1, + "uniqueItems": true + }, + "rows": { + "description": "The rows of the plate", + "type": "array", + "items": { + "type": "object", + "properties": { + "name": { + "description": "The row name", + "type": "string", + "pattern": "^[A-Za-z0-9]+$" + } + }, + "required": [ + "name" + ] + }, + "minItems": 1, + "uniqueItems": true + }, + "wells": { + "description": "The wells of the plate", + "type": "array", + "items": { + "type": "object", + "properties": { + "path": { + "description": "The path to the well subgroup", + "type": "string", + "pattern": "^[A-Za-z0-9]+/[A-Za-z0-9]+$" + }, + "rowIndex": { + "description": "The index of the well in the rows list", + "type": "integer", + "minimum": 0 + }, + "columnIndex": { + "description": "The index of the well in the columns list", + "type": "integer", + "minimum": 0 + } + }, + "required": [ + "path", + "rowIndex", + "columnIndex" + ] + }, + "minItems": 1, + "uniqueItems": true + } + }, + "required": [ + "columns", + "rows", + "wells" + ] + }, + "version": { + "$ref": "https://ngff.openmicroscopy.org/0.5/schemas/_version.schema" + } + }, + "required": [ + "plate", + "version" + ] + } + }, + "required": [ + "ome" + ] +} diff --git a/latest/schemas/strict_image.schema b/latest/schemas/strict_image.schema new file mode 100644 index 00000000..042790e7 --- /dev/null +++ b/latest/schemas/strict_image.schema @@ -0,0 +1,25 @@ +{ + "$id": "https://ngff.openmicroscopy.org/0.5/schemas/strict_image.schema", + "allOf": [ + { + "$ref": "https://ngff.openmicroscopy.org/0.5/schemas/image.schema" + }, + { + "properties": { + "ome": { + "properties": { + "multiscales": { + "items": { + "required": [ + "metadata", + "type", + "name" + ] + } + } + } + } + } + } + ] +} diff --git a/latest/schemas/strict_label.schema b/latest/schemas/strict_label.schema new file mode 100644 index 00000000..f1ec4db5 --- /dev/null +++ b/latest/schemas/strict_label.schema @@ -0,0 +1,21 @@ +{ + "$id": "https://ngff.openmicroscopy.org/0.5/schemas/strict_label.schema", + "allOf": [ + { + "$ref": "https://ngff.openmicroscopy.org/0.5/schemas/label.schema" + }, + { + "properties": { + "ome": { + "properties": { + "image-label": { + "required": [ + "colors" + ] + } + } + } + } + } + ] +} diff --git a/latest/schemas/strict_plate.schema b/latest/schemas/strict_plate.schema new file mode 100644 index 00000000..ce678ce8 --- /dev/null +++ b/latest/schemas/strict_plate.schema @@ -0,0 +1,31 @@ +{ + "$id": "https://ngff.openmicroscopy.org/0.5/schemas/strict_plate.schema", + "allOf": [ + { + "$ref": "https://ngff.openmicroscopy.org/0.5/schemas/plate.schema" + }, + { + "properties": { + "ome": { + "properties": { + "plate": { + "properties": { + "acquisitions": { + "items": { + "required": [ + "name", + "maximumfieldcount" + ] + } + } + }, + "required": [ + "name" + ] + } + } + } + } + } + ] +} diff --git a/latest/schemas/strict_well.schema b/latest/schemas/strict_well.schema new file mode 100644 index 00000000..43cb58cb --- /dev/null +++ b/latest/schemas/strict_well.schema @@ -0,0 +1,8 @@ +{ + "$id": "https://ngff.openmicroscopy.org/0.5/schemas/strict_well.schema", + "allOf": [ + { + "$ref": "https://ngff.openmicroscopy.org/0.5/schemas/well.schema" + } + ] +} diff --git a/latest/schemas/well.schema b/latest/schemas/well.schema new file mode 100644 index 00000000..447f51df --- /dev/null +++ b/latest/schemas/well.schema @@ -0,0 +1,56 @@ +{ + "$schema": "https://json-schema.org/draft/2020-12/schema", + "$id": "https://ngff.openmicroscopy.org/0.5/schemas/well.schema", + "title": "OME-Zarr well schema", + "description": "JSON from OME-Zarr zarr.json", + "type": "object", + "properties": { + "ome": { + "description": "The versioned OME-Zarr Metadata namespace", + "type": "object", + "properties": { + "well": { + "type": "object", + "properties": { + "images": { + "description": "The fields of view for this well", + "type": "array", + "items": { + "type": "object", + "properties": { + "acquisition": { + "description": "A unique identifier within the context of the plate", + "type": "integer" + }, + "path": { + "description": "The path for this field of view subgroup", + "type": "string", + "pattern": "^[A-Za-z0-9]+$" + } + }, + "required": [ + "path" + ] + }, + "minItems": 1, + "uniqueItems": true + } + }, + "required": [ + "images" + ] + }, + "version": { + "$ref": "https://ngff.openmicroscopy.org/0.5/schemas/_version.schema" + } + }, + "required": [ + "well", + "version" + ] + } + }, + "required": [ + "ome" + ] +} diff --git a/latest/tests/image_suite.json b/latest/tests/image_suite.json new file mode 100644 index 00000000..df359ce4 --- /dev/null +++ b/latest/tests/image_suite.json @@ -0,0 +1,1040 @@ +{ + "description": "TBD", + "schema": { + "id": "schemas/image.schema" + }, + "tests": [ + { + "formerly": "valid/mismatch_axes_units.json", + "description": "TBD", + "data": { + "ome": { + "version": "0.5", + "multiscales": [ + { + "axes": [ + { + "name": "t", + "type": "time", + "unit": "micrometer" + }, + { + "name": "y", + "type": "space", + "unit": "micrometer" + }, + { + "name": "x", + "type": "space", + "unit": "micrometer" + } + ], + "datasets": [ + { + "path": "0", + "coordinateTransformations": [ + { + "scale": [0.13, 0.13], + "type": "scale" + } + ] + } + ] + } + ] + } + }, + "valid": true + }, + { + "formerly": "valid/untyped_axes.json", + "description": "TBD", + "data": { + "ome": { + "version": "0.5", + "multiscales": [ + { + "axes": [ + { + "name": "angle" + }, + { + "name": "y", + "type": "space", + "unit": "micrometer" + }, + { + "name": "x", + "type": "space", + "unit": "micrometer" + } + ], + "datasets": [ + { + "path": "0", + "coordinateTransformations": [ + { + "scale": [1, 1, 1], + "type": "scale" + } + ] + } + ] + } + ] + } + }, + "valid": true + }, + { + "formerly": "valid/invalid_axis_units.json", + "description": "TBD", + "data": { + "ome": { + "version": "0.5", + "multiscales": [ + { + "axes": [ + { + "name": "y", + "type": "space", + "unit": "micron" + }, + { + "name": "x", + "type": "space", + "unit": "micrometer" + } + ], + "datasets": [ + { + "path": "0", + "coordinateTransformations": [ + { + "scale": [0.13, 0.13], + "type": "scale" + } + ] + } + ] + } + ] + } + }, + "valid": true + }, + { + "formerly": "valid/missing_name.json", + "description": "TBD", + "data": { + "ome": { + "version": "0.5", + "multiscales": [ + { + "datasets": [ + { + "path": "path/to/0", + "coordinateTransformations": [ + { + "type": "scale", + "scale": [1, 1] + } + ] + } + ], + "type": "gaussian", + "metadata": { + "method": "skimage.transform.pyramid_gaussian", + "version": "0.16.1", + "args": ["true", "false"], + "kwargs": { + "multichannel": true + } + }, + "axes": [ + { + "name": "y", + "type": "space", + "unit": "micrometer" + }, + { + "name": "x", + "type": "space", + "unit": "micrometer" + } + ] + } + ] + } + }, + "valid": true + }, + { + "formerly": "valid/custom_type_axes.json", + "description": "TBD", + "data": { + "ome": { + "version": "0.5", + "multiscales": [ + { + "axes": [ + { + "name": "angle", + "type": "custom" + }, + { + "name": "y", + "type": "space", + "unit": "micrometer" + }, + { + "name": "x", + "type": "space", + "unit": "micrometer" + } + ], + "datasets": [ + { + "path": "0", + "coordinateTransformations": [ + { + "scale": [1, 1, 1], + "type": "scale" + } + ] + } + ] + } + ] + } + }, + "valid": true + }, + { + "formerly": "invalid/duplicate_axes.json", + "description": "TBD", + "data": { + "ome": { + "version": "0.5", + "multiscales": [ + { + "axes": [ + { + "name": "x", + "type": "space", + "unit": "micrometer" + }, + { + "name": "x", + "type": "space", + "unit": "micrometer" + } + ], + "datasets": [ + { + "path": "0", + "coordinateTransformations": [ + { + "scale": [1, 1], + "type": "scale" + } + ] + } + ] + } + ] + } + }, + "valid": false + }, + { + "formerly": "invalid/missing_space_axes.json", + "description": "TBD", + "data": { + "ome": { + "version": "0.5", + "multiscales": [ + { + "axes": [ + { + "name": "t", + "type": "time" + }, + { + "name": "c", + "type": "channel" + } + ], + "datasets": [ + { + "path": "0", + "coordinateTransformations": [ + { + "scale": [1, 1], + "type": "scale" + } + ] + } + ] + } + ] + } + }, + "valid": false + }, + { + "formerly": "invalid/invalid_transformation_type.json", + "description": "TBD", + "data": { + "ome": { + "version": "0.5", + "multiscales": [ + { + "axes": [ + { + "name": "y", + "type": "space", + "unit": "micrometer" + }, + { + "name": "x", + "type": "space", + "unit": "micrometer" + } + ], + "datasets": [ + { + "path": "0", + "coordinateTransformations": [ + { + "scale": [1, 1], + "type": "translation" + } + ] + } + ] + } + ] + } + }, + "valid": false + }, + { + "formerly": "invalid/missing_scale.json", + "description": "TBD", + "data": { + "ome": { + "version": "0.5", + "multiscales": [ + { + "axes": [ + { + "name": "y", + "type": "space", + "unit": "micrometer" + }, + { + "name": "x", + "type": "space", + "unit": "micrometer" + } + 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"id": 0, + "maximumfieldcount": "0" + } + ], + "columns": [ + { + "name": "A" + } + ], + "rows": [ + { + "name": "1" + } + ], + "wells": [ + { + "path": "A/1", + "rowIndex": 0, + "columnIndex": 0 + } + ] + } + } + }, + "valid": false + }, + { + "formerly": "plate/acquisition_zero_maximumfieldcount", + "data": { + "ome": { + "version": "0.5", + "plate": { + "acquisitions": [ + { + "id": 0, + "maximumfieldcount": 0 + } + ], + "columns": [ + { + "name": "A" + } + ], + "rows": [ + { + "name": "1" + } + ], + "wells": [ + { + "path": "A/1", + "rowIndex": 0, + "columnIndex": 0 + } + ] + } + } + }, + "valid": false + }, + { + "formerly": "plate/acquisition_noninteger_starttime", + "data": { + "ome": { + "version": "0.5", + "plate": { + "acquisitions": [ + { + "id": 0, + "starttime": "2022-05-13T13:48:06+00:00" + } + ], + "columns": [ + { + "name": "A" + } + ], + "rows": [ + { + "name": "1" + } + ], + "wells": [ + { + "path": "A/1", + "rowIndex": 0, + "columnIndex": 0 + } + ] + } + } + }, + "valid": false + }, + { + "formerly": "plate/acquisition_negative_starttime", + "data": { + "ome": { + "version": "0.5", + "plate": { + "acquisitions": [ + { + "id": 0, + "starttime": -1 + } + ], + "columns": [ + { + "name": "A" + } + ], + "rows": [ + { + "name": "1" + } + ], + "wells": [ + { + "path": "A/1", + "rowIndex": 0, + "columnIndex": 0 + } + ] + } + } + }, + "valid": false + }, + { + "formerly": "plate/acquisition_noninteger_endtime", + "data": { + "ome": { + "version": "0.5", + "plate": { + "acquisitions": [ + { + "id": 0, + "endtime": "2022-05-13T13:48:06+00:00" + } + ], + "columns": [ + { + "name": "A" + } + ], + "rows": [ + { + "name": "1" + } + ], + "wells": [ + { + "path": "A/1", + "rowIndex": 0, + "columnIndex": 0 + } + ] + } + } + }, + "valid": false + }, + { + "formerly": "plate/negative_endtime", + "data": { + "ome": { + "version": "0.5", + "plate": { + "acquisitions": [ + { + "id": 0, + "endtime": -1 + } + ], + "columns": [ + { + "name": "A" + } + ], + "rows": [ + { + "name": "1" + } + ], + "wells": [ + { + "path": "A/1", + "rowIndex": 0, + "columnIndex": 0 + } + ] + } + } + }, + "valid": false + }, + { + "formerly": "plate/zero_field_count", + "data": { + "ome": { + "version": "0.5", + "plate": { + "columns": [ + { + "name": "A" + } + ], + "field_count": 0, + "rows": [ + { + "name": "1" + } + ], + "wells": [ + { + "path": "A/1", + "rowIndex": 0, + "columnIndex": 0 + } + ] + } + } + }, + "valid": false + } + ] +} diff --git a/latest/tests/strict_image_suite.json b/latest/tests/strict_image_suite.json new file mode 100644 index 00000000..b52fd2d3 --- /dev/null +++ b/latest/tests/strict_image_suite.json @@ -0,0 +1,341 @@ +{ + "description": "TBD", + "schema": { + "id": "schemas/strict_image.schema" + }, + "tests": [ + { + "formerly": "valid_strict/multiscales_example.json", + "description": "TBD", + "data": { + "ome": { + "version": "0.5", + "multiscales": [ + { + "name": "example", + "axes": [ + { + "name": "t", + "type": "time", + "unit": "millisecond" + }, + { + "name": "c", + "type": "channel" + }, + { + "name": "z", + "type": "space", + "unit": "micrometer" + }, + { + "name": "y", + "type": "space", + "unit": "micrometer" + }, + { + "name": "x", + "type": "space", + "unit": "micrometer" + } + ], + "datasets": [ + { + "path": "0", + "coordinateTransformations": [ + { + "type": "scale", + "scale": [1.0, 1.0, 0.5, 0.5, 0.5] + } + ] + }, + { + "path": "1", + "coordinateTransformations": [ + { + "type": "scale", + "scale": [1.0, 1.0, 1.0, 1.0, 1.0] + } + ] + }, + { + "path": "2", + "coordinateTransformations": [ + { + "type": "scale", + "scale": [1.0, 1.0, 2.0, 2.0, 2.0] + } + ] + } + ], + "coordinateTransformations": [ + { + "type": "scale", + "scale": [0.1, 1.0, 1.0, 1.0, 1.0] + } + ], + "type": "gaussian", + "metadata": { + "description": "the fields in metadata depend on the downscaling implementation. Here, the parameters passed to the skimage function are given", + "method": "skimage.transform.pyramid_gaussian", + "version": "0.16.1", + "args": "[true]", + "kwargs": { + "multichannel": true + } + } + } + ] + } + }, + "valid": true + }, + { + "formerly": "valid_strict/multiscales_transformations.json", + "description": "TBD", + "data": { + "ome": { + "version": "0.5", + "multiscales": [ + { + "axes": [ + { + "name": "y", + "type": "space", + "unit": "micrometer" + }, + { + "name": "x", + "type": "space", + "unit": "micrometer" + } + ], + "datasets": [ + { + "path": "0", + "coordinateTransformations": [ + { + "scale": [1, 1], + "type": "scale" + } + ] + } + ], + "coordinateTransformations": [ + { + "scale": [10, 10], + "type": "scale" + } + ], + "name": "image_with_coordinateTransformations", + "type": "foo", + "metadata": { + "key": "value" + } + } + ] + } + }, + "valid": true + }, + { + "formerly": "valid_strict/image_metadata.json", + "description": "TBD", + "data": { + "ome": { + "version": "0.5", + "@id": "top", + "@type": "ngff:Image", + "multiscales": [ + { + "@id": "inner", + "name": "example", + "datasets": [ + { + "path": "path/to/0", + "coordinateTransformations": [ + { + "type": "scale", + "scale": [1, 1] + } + ] + } + ], + "type": "gaussian", + "metadata": { + "method": "skimage.transform.pyramid_gaussian", + "version": "0.16.1", + "args": ["true", "false"], + "kwargs": { + "multichannel": true + } + }, + "axes": [ + { + "name": "y", + "type": "space", + "unit": "micrometer" + }, + { + "name": "x", + "type": "space", + "unit": "micrometer" + } + ] + } + ] + } + }, + "valid": true + }, + { + "formerly": "valid_strict/image.json", + "description": "TBD", + "data": { + "ome": { + "version": "0.5", + "multiscales": [ + { + "axes": [ + { + "name": "y", + "type": "space", + "unit": "micrometer" + }, + { + "name": "x", + "type": "space", + "unit": "micrometer" + } + ], + "datasets": [ + { + "path": "0", + "coordinateTransformations": [ + { + "scale": [1, 1], + "type": "scale" + } + ] + } + ], + "name": "simple_image", + "type": "foo", + "metadata": { + "key": "value" + } + } + ] + } + }, + "valid": true + }, + { + "formerly": "valid_strict/image_omero.json", + "description": "TBD", + "data": { + "ome": { + "version": "0.5", + "multiscales": [ + { + "axes": [ + { + "name": "t", + "type": "time" + }, + { + "name": "c", + "type": "channel" + }, + { + "name": "z", + "type": "space", + "unit": "micrometer" + }, + { + "name": "y", + "type": "space", + "unit": "micrometer" + }, + { + "name": "x", + "type": "space", + "unit": "micrometer" + } + ], + "datasets": [ + { + "path": "0", + "coordinateTransformations": [ + { + "scale": [1, 1, 0.5, 0.13, 0.13], + "type": "scale" + }, + { + "translation": [0, 9, 0.5, 25.74, 21.58], + "type": "translation" + } + ] + }, + { + "path": "1", + "coordinateTransformations": [ + { + "scale": [1, 1, 1, 0.26, 0.26], + "type": "scale" + } + ] + } + ], + "name": "image_with_omero_metadata", + "type": "foo", + "metadata": { + "key": "value" + } + } + ], + "omero": { + "channels": [ + { + "active": true, + "coefficient": 1.0, + "color": "00FF00", + "family": "linear", + "inverted": false, + "label": "FITC", + "window": { + "end": 813.0, + "max": 870.0, + "min": 102.0, + "start": 82.0 + } + }, + { + "active": true, + "coefficient": 1.0, + "color": "FF0000", + "family": "linear", + "inverted": false, + "label": "RD-TR-PE", + "window": { + "end": 815.0, + "max": 441.0, + "min": 129.0, + "start": 78.0 + } + } + ], + "id": 1, + "rdefs": { + "defaultT": 0, + "defaultZ": 2, + "model": "color" + }, + "version": "0.5-dev" + } + } + }, + "valid": true + } + ] +} diff --git a/latest/tests/strict_label_suite.json b/latest/tests/strict_label_suite.json new file mode 100644 index 00000000..1b3535c2 --- /dev/null +++ b/latest/tests/strict_label_suite.json @@ -0,0 +1,18 @@ +{ + "description": "Tests for the strict image-label JSON schema", + "schema": { + "id": "schemas/strict_label.schema" + }, + "tests": [ + { + "formerly": "image-label/no_colors", + "data": { + "ome": { + "version": "0.5", + "image-label": {} + } + }, + "valid": false + } + ] +} diff --git a/latest/tests/strict_plate_suite.json b/latest/tests/strict_plate_suite.json new file mode 100644 index 00000000..7cea0747 --- /dev/null +++ b/latest/tests/strict_plate_suite.json @@ -0,0 +1,171 @@ +{ + "description": "Tests for the strict plate JSON schema", + "schema": { + "id": "schemas/strict_plate.schema" + }, + "tests": [ + { + "formerly": "plate/strict_no_acquisitions", + "data": { + "ome": { + "version": "0.5", + "plate": { + "columns": [ + { + "name": "A" + } + ], + "name": "test plate", + "rows": [ + { + "name": "1" + } + ], + "wells": [ + { + "path": "A/1", + "rowIndex": 0, + "columnIndex": 0 + } + ] + } + } + }, + "valid": true + }, + { + "formerly": "plate/missing_name", + "data": { + "ome": { + "version": "0.5", + "plate": { + "columns": [ + { + "name": "A" + } + ], + "rows": [ + { + "name": "1" + } + ], + "wells": [ + { + "path": "A/1", + "rowIndex": 0, + "columnIndex": 0 + } + ] + } + } + }, + "valid": false + }, + { + "formerly": "plate/strict_acquisitions", + "data": { + "ome": { + "version": "0.5", + "plate": { + "acquisitions": [ + { + "id": 0, + "name": "0", + "maximumfieldcount": 1 + } + ], + "columns": [ + { + "name": "A" + } + ], + "name": "test plate", + "rows": [ + { + "name": "1" + } + ], + "wells": [ + { + "path": "A/1", + "rowIndex": 0, + "columnIndex": 0 + } + ] + } + } + }, + "valid": true + }, + { + "formerly": "plate/missing_acquisition_name", + "data": { + "ome": { + "version": "0.5", + "plate": { + "acquisitions": [ + { + "id": 0, + "maximumfieldcount": 1 + } + ], + "columns": [ + { + "name": "A" + } + ], + "name": "test plate", + "rows": [ + { + "name": "1" + } + ], + "wells": [ + { + "path": "A/1", + "rowIndex": 0, + "columnIndex": 0 + } + ] + } + } + }, + "valid": false + }, + { + "formerly": "plate/missing_acquisition_maximumfieldcount", + "data": { + "ome": { + "version": "0.5", + "plate": { + "acquisitions": [ + { + "id": 0, + "name": "0" + } + ], + "columns": [ + { + "name": "A" + } + ], + "name": "test plate", + "rows": [ + { + "name": "1" + } + ], + "wells": [ + { + "path": "A/1", + "rowIndex": 0, + "columnIndex": 0 + } + ] + } + } + }, + "valid": false + } + ] +} diff --git a/latest/tests/strict_well_suite.json b/latest/tests/strict_well_suite.json new file mode 100644 index 00000000..f56b6c24 --- /dev/null +++ b/latest/tests/strict_well_suite.json @@ -0,0 +1,41 @@ +{ + "description": "Tests for the strict well JSON schema", + "schema": { + "id": "schemas/strict_well.schema" + }, + "tests": [ + { + "formerly": "well/strict_no_acquisitions", + "data": { + "ome": { + "version": "0.5", + "well": { + "images": [ + { + "path": "0" + } + ] + } + } + }, + "valid": true + }, + { + "formerly": "plate/strict_acquisitions", + "data": { + "ome": { + "version": "0.5", + "well": { + "images": [ + { + "acquisition": 0, + "path": "0" + } + ] + } + } + }, + "valid": true + } + ] +} diff --git a/latest/tests/test_validation.py b/latest/tests/test_validation.py new file mode 100644 index 00000000..b9c7c929 --- /dev/null +++ b/latest/tests/test_validation.py @@ -0,0 +1,125 @@ +import json +import glob +import os + +from dataclasses import dataclass +from typing import List + +import pytest + +from jsonschema import RefResolver, Draft202012Validator as Validator +from jsonschema.exceptions import ValidationError + +schema_store = {} +for schema_filename in glob.glob("schemas/*"): + with open(schema_filename) as f: + schema = json.load(f) + schema_store[schema["$id"]] = schema + +GENERIC_SCHEMA = schema_store[ + "https://ngff.openmicroscopy.org/0.5/schemas/ome_zarr.schema" +] + +print(schema_store) + + +@dataclass +class Suite: + schema: dict + data: dict + valid: bool = True + + def validate(self, validator) -> None: + if not self.valid: + with pytest.raises(ValidationError): + validator.validate(self.data) + else: + validator.validate(self.data) + + def maybe_validate(self, validator) -> None: + if self.valid: + validator.validate(self.data) + + +def pytest_generate_tests(metafunc): + """ + Generates tests for the examples/ as well as tests/ subdirectories. + + Examples: + These tests evaluate all of the files under the examples/ directory + using the configuration in the provided config file in order detect + what should be run. It is assumed that all files are valid and complete + so that they can be wholly included into the specification. The + .config.json file in each directory defines which schema will be used. + + Validation: + These test consumes https://github.com/json-schema-org/JSON-Schema-Test-Suite#structure-of-a-test + styled JSON tests. Metadata in each test defines which schema is used + and whether or not the block is considered valid. + """ + if "suite" in metafunc.fixturenames: + suites: List[Schema] = [] + ids: List[str] = [] + + # Validation + for filename in glob.glob("tests/*.json"): + with open(filename) as o: + suite = json.load(o) + schema = suite["schema"] + with open(schema["id"]) as f: + schema = json.load(f) + for test in suite["tests"]: + ids.append("validate_" + str(test["formerly"]).split("/")[-1][0:-5]) + suites.append(Suite(schema, test["data"], test["valid"])) + + # Examples + for config_filename in glob.glob("examples/*/.config.json"): + with open(config_filename) as o: + data = json.load(o) + schema = data["schema"] + with open(schema) as f: + schema = json.load(f) + example_folder = os.path.dirname(config_filename) + for filename in glob.glob(f"{example_folder}/*.json"): + with open(filename) as f: + # Strip comments + data = "".join( + line for line in f if not line.lstrip().startswith("//") + ) + data = json.loads(data) + data = data["attributes"] # Only validate the attributes object + ids.append("example_" + str(filename).split("/")[-1][0:-5]) + suites.append(Suite(schema, data, True)) # Assume true + + metafunc.parametrize("suite", suites, ids=ids, indirect=True) + + +@pytest.fixture +def suite(request): + return request.param + + +def test_run(suite): + resolver = RefResolver.from_schema(suite.schema, store=schema_store) + validator = Validator(suite.schema, resolver=resolver) + suite.validate(validator) + + +def test_generic_run(suite): + resolver = RefResolver.from_schema(GENERIC_SCHEMA, store=schema_store) + validator = Validator(GENERIC_SCHEMA, resolver=resolver) + suite.maybe_validate(validator) + + +def test_example_configs(): + """ + Test that all example folders have a config file + """ + missing = [] + for subdir in os.walk("examples"): + has_examples = glob.glob(f"{subdir[0]}/*.json") + has_config = glob.glob(f"{subdir[0]}/.config.json") + if has_examples and not has_config: + missing.append(subdir[0]) + if missing: + raise Exception(f"Directories missing configs: {missing}") diff --git a/latest/tests/well_suite.json b/latest/tests/well_suite.json new file mode 100644 index 00000000..7fbf8ca2 --- /dev/null +++ b/latest/tests/well_suite.json @@ -0,0 +1,80 @@ +{ + "description": "Tests for the well JSON schema", + "schema": { + "id": "schemas/well.schema" + }, + "tests": [ + { + "formerly": "well/minimal_no_acquisition", + "data": { + "ome": { + "version": "0.5", + "well": { + "images": [ + { + "path": "0" + } + ] + } + } + }, + "valid": true + }, + { + "formerly": "well/minimal_acquisitions", + "data": { + "ome": { + "version": "0.5", + "well": { + "images": [ + { + "acquisition": 1, + "path": "0" + } + ] + } + } + }, + "valid": true + }, + { + "formerly": "well/empty_images", + "data": { + "well": { + "images": [] + } + }, + "valid": false + }, + { + "formerly": "well/duplicate_images", + "data": { + "well": { + "images": [ + { + "path": "0" + }, + { + "path": "0" + } + ] + } + }, + "valid": false + }, + { + "formerly": "well/non_integer_acquisition_id", + "data": { + "well": { + "images": [ + { + "acquisition": "0", + "path": "0" + } + ] + } + }, + "valid": false + } + ] +} diff --git a/latest/tox.ini b/latest/tox.ini new file mode 100644 index 00000000..632ca64e --- /dev/null +++ b/latest/tox.ini @@ -0,0 +1,10 @@ +[tox] +envlist = v04 +skipsdist = True + +[testenv] +deps = + pytest + jsonschema +commands = + pytest tests --color=yes --basetemp={envtmpdir} {posargs:-v} \ No newline at end of file From 9ed7f06abab58e424d51f0773c285a5c53e1d314 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 29 Nov 2024 21:31:12 +0000 Subject: [PATCH 2/4] Add contributing + changelog guidelines --- contributing/index.md | 6 ++++ latest/index.bs | 82 +++++++++++++++++++++++-------------------- 2 files changed, 50 insertions(+), 38 deletions(-) create mode 100644 contributing/index.md diff --git a/contributing/index.md b/contributing/index.md new file mode 100644 index 00000000..9c2f904a --- /dev/null +++ b/contributing/index.md @@ -0,0 +1,6 @@ +# Contributing + +## Minor changes or clarifications + +Minor changes or clarifications to the specification should be made against the copy in the `latest` folder. +Please add a changelog entry explaining clearly the change you are making, so when a new version of the specifciation is released it is clear what has changed. diff --git a/latest/index.bs b/latest/index.bs index 474119e3..87fb06cb 100644 --- a/latest/index.bs +++ b/latest/index.bs @@ -52,8 +52,8 @@ Storage format {#storage-format} OME-Zarr is implemented using the Zarr format as defined by the [version 3 of the Zarr specification](https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html). -All features of the Zarr format including codecs, chunk grids, chunk -key encodings, data types and storage transformers may be used with +All features of the Zarr format including codecs, chunk grids, chunk +key encodings, data types and storage transformers may be used with OME-Zarr unless explicitly disallowed in this specification. An overview of the layout of an OME-Zarr fileset should make @@ -87,7 +87,7 @@ Note that the number of dimensions is variable between 2 and 5 and that axis nam │ ├── zarr.json # All image arrays must be up to 5-dimensional │ │ # with the axis of type time before type channel, before spatial axes. │ │ - │ └─ ... # Chunks are stored conforming to the Zarr array specification and + │ └─ ... # Chunks are stored conforming to the Zarr array specification and │ # metadata as specified in the array's `zarr.json`. │ └── labels @@ -106,7 +106,7 @@ Note that the number of dimensions is variable between 2 and 5 and that axis nam │ ├── 0 # Each multiscale level is stored as a separate Zarr array, as above, but only integer values └── ... # are supported. - + @@ -143,7 +143,7 @@ A well group SHOULD NOT be present if there are no images in the well. │ │ ├── 0 # First field of view of well A1 │ │ │ │ │ │ │ ├── zarr.json # Implements "multiscales", "omero" - │ │ │ ├── 0 # Resolution levels + │ │ │ ├── 0 # Resolution levels │ │ │ ├── ... │ │ │ └── labels # Labels (optional) │ │ └── ... # Other fields of view @@ -154,11 +154,11 @@ A well group SHOULD NOT be present if there are no images in the well. OME-Zarr Metadata {#metadata} ============================= -The "OME-Zarr Metadata" contains metadata keys as specified below +The "OME-Zarr Metadata" contains metadata keys as specified below for discovering certain types of data, especially images. The OME-Zarr Metadata is stored in the various `zarr.json` files throughout the above array -hierarchy. In this file, the metadata is stored under the namespaced key +hierarchy. In this file, the metadata is stored under the namespaced key `ome` in `attributes`. The version of the OME-Zarr Metadata is denoted as a string in the `version` attribute within the `ome` namespace. @@ -293,8 +293,8 @@ The transformations in the list are applied sequentially and in order. "multiscales" metadata {#multiscale-md} --------------------------------------- -Metadata about an image can be found under the "multiscales" key in the group-level OME-Zarr Metadata. -Here, image refers to 2 to 5 dimensional data representing image or volumetric data with optional time or channel axes. +Metadata about an image can be found under the "multiscales" key in the group-level OME-Zarr Metadata. +Here, image refers to 2 to 5 dimensional data representing image or volumetric data with optional time or channel axes. It is stored in a multiple resolution representation. "multiscales" contains a list of dictionaries where each entry describes a multiscale image. @@ -384,18 +384,18 @@ for more information. "labels" metadata {#labels-md} ------------------------------ -In OME-Zarr, Zarr arrays representing pixel-annotation data are stored in a group called "labels". Some applications--notably image segmentation--produce -a new image that is in the same coordinate system as a corresponding multiscale image (usually having the same dimensions and coordinate transformations). -This new image is composed of integer values corresponding to certain labels with custom meanings. For example, pixels take the value 1 or 0 -if the corresponding pixel in the original image represents cellular space or intercellular space, respectively. -Such an image is referred to in this specification as a 'label image'. +In OME-Zarr, Zarr arrays representing pixel-annotation data are stored in a group called "labels". Some applications--notably image segmentation--produce +a new image that is in the same coordinate system as a corresponding multiscale image (usually having the same dimensions and coordinate transformations). +This new image is composed of integer values corresponding to certain labels with custom meanings. For example, pixels take the value 1 or 0 +if the corresponding pixel in the original image represents cellular space or intercellular space, respectively. +Such an image is referred to in this specification as a 'label image'. -The "labels" group is nested within an image group, at the same level of the Zarr hierarchy as the resolution levels for the original image. -The "labels" group is not itself an image; it contains images. The pixels of the label images MUST be integer data types, i.e. one of -[`uint8`, `int8`, `uint16`, `int16`, `uint32`, `int32`, `uint64`, `int64`]. Intermediate groups between "labels" and the images within it are allowed, +The "labels" group is nested within an image group, at the same level of the Zarr hierarchy as the resolution levels for the original image. +The "labels" group is not itself an image; it contains images. The pixels of the label images MUST be integer data types, i.e. one of +[`uint8`, `int8`, `uint16`, `int16`, `uint32`, `int32`, `uint64`, `int64`]. Intermediate groups between "labels" and the images within it are allowed, but these MUST NOT contain metadata. Names of the images in the "labels" group are arbitrary. -The OME-Zarr Metadata in the `zarr.json` file associated with the "labels" group MUST contain a JSON object with the key `labels`, whose value is a JSON array of paths to the +The OME-Zarr Metadata in the `zarr.json` file associated with the "labels" group MUST contain a JSON object with the key `labels`, whose value is a JSON array of paths to the labeled multiscale image(s). All label images SHOULD be listed within this metadata file. For example: ```json @@ -412,32 +412,32 @@ labeled multiscale image(s). All label images SHOULD be listed within this metad } ``` -The `zarr.json` file for the label image MUST implement the multiscales specification. Within the `multiscales` object, the JSON array -associated with the `datasets` key MUST have the same number of entries (scale levels) as the original unlabeled image. +The `zarr.json` file for the label image MUST implement the multiscales specification. Within the `multiscales` object, the JSON array +associated with the `datasets` key MUST have the same number of entries (scale levels) as the original unlabeled image. -In addition to the `multiscales` key, the OME-Zarr Metadata in this image-level `zarr.json` file SHOULD contain another key, `image-label`, -whose value is also a JSON object. The `image-label` object stores information about the display colors, source image, and optionally, -further arbitrary properties of the label image. That `image-label` object SHOULD contain the following keys: first, a `colors` key, -whose value MUST be a JSON array describing color information for the unique label values. Second, a `version` key, whose value MUST be a +In addition to the `multiscales` key, the OME-Zarr Metadata in this image-level `zarr.json` file SHOULD contain another key, `image-label`, +whose value is also a JSON object. The `image-label` object stores information about the display colors, source image, and optionally, +further arbitrary properties of the label image. That `image-label` object SHOULD contain the following keys: first, a `colors` key, +whose value MUST be a JSON array describing color information for the unique label values. Second, a `version` key, whose value MUST be a string specifying the version of the OME-Zarr `image-label` schema. -Conforming readers SHOULD display labels using the colors specified by the `colors` JSON array, as follows. This array contains one -JSON object for each unique custom label. Each of these objects MUST contain the `label-value` key, whose value MUST be the integer -corresponding to a particular label. In addition to the `label-value` key, the objects in this array MAY contain an `rgba` key whose -value MUST be an array of four integers between 0 and 255, inclusive. These integers represent the `uint8` values of red, green, and -blue that comprise the final color to be displayed at the pixels with this label. The fourth integer in the `rgba` array represents alpha, -or the opacity of the color. Additional keys under `colors` are allowed. +Conforming readers SHOULD display labels using the colors specified by the `colors` JSON array, as follows. This array contains one +JSON object for each unique custom label. Each of these objects MUST contain the `label-value` key, whose value MUST be the integer +corresponding to a particular label. In addition to the `label-value` key, the objects in this array MAY contain an `rgba` key whose +value MUST be an array of four integers between 0 and 255, inclusive. These integers represent the `uint8` values of red, green, and +blue that comprise the final color to be displayed at the pixels with this label. The fourth integer in the `rgba` array represents alpha, +or the opacity of the color. Additional keys under `colors` are allowed. Next, the `image-label` object MAY contain the following keys: a `properties` key, and a `source` key. -Like the `colors` key, the value of the `properties` key MUST be an array of JSON objects describing the set of unique possible pixel values. -Each object in the `properties` array MUST contain the `label-value` key, whose value again MUST be an integer specifying the pixel value for that label. -Additionally, an arbitrary number of key-value pairs MAY be present for each label value, denoting arbitrary metadata associated with that label. +Like the `colors` key, the value of the `properties` key MUST be an array of JSON objects describing the set of unique possible pixel values. +Each object in the `properties` array MUST contain the `label-value` key, whose value again MUST be an integer specifying the pixel value for that label. +Additionally, an arbitrary number of key-value pairs MAY be present for each label value, denoting arbitrary metadata associated with that label. Label-value objects within the `properties` array do not need to have the same keys. -The value of the `source` key MUST be a JSON object containing information about the original image from which the label image derives. -This object MAY include a key `image`, whose value MUST be a string specifying the relative path to a Zarr image group. -The default value is `../../` since most labeled images are stored in a "labels" group that is nested within the original image group. +The value of the `source` key MUST be a JSON object containing information about the original image from which the label image derives. +This object MAY include a key `image`, whose value MUST be a string specifying the relative path to a Zarr image group. +The default value is `../../` since most labeled images are stored in a "labels" group that is nested within the original image group. Here is an example of a simple `image-label` object for a label image in which 0s and 1s represent intercellular and cellular space, respectively: @@ -446,8 +446,8 @@ path: examples/label_strict/colors_properties.json highlight: json -In this case, the pixels consisting of a 0 in the Zarr array will be displayed as 50% blue and 50% opacity. Pixels with a 1 in the Zarr array, -which correspond to cellular space, will be displayed as 50% green and 50% opacity. +In this case, the pixels consisting of a 0 in the Zarr array will be displayed as 50% blue and 50% opacity. Pixels with a 1 in the Zarr array, +which correspond to cellular space, will be displayed as 50% green and 50% opacity. "plate" metadata {#plate-md} ---------------------------- @@ -564,6 +564,12 @@ Multi-word keys in this specification should use the `camelCase` style. NB: some parts of the specification don't obey this convention as they were added before this was adopted, but they should be updated in due course. +Changelog +========= + +Next version (unreleased) +------------------------- + Implementations {#implementations} ================================== From 1e2e5b49afcee8fdc712e8bcec5b1cb9dbef2756 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 29 Nov 2024 21:32:12 +0000 Subject: [PATCH 3/4] Add contributing to ToC --- index.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/index.rst b/index.rst index 85db7d2b..ce822a7c 100644 --- a/index.rst +++ b/index.rst @@ -19,6 +19,7 @@ Sample OME-Zarr datasets provided by the community can be found under :doc:`data about/index community/index + contributing/index data/index publications/index specifications/index From befc8dadb7556198d8e8e23fbb345a998444af06 Mon Sep 17 00:00:00 2001 From: David Stansby Date: Fri, 29 Nov 2024 21:37:08 +0000 Subject: [PATCH 4/4] Clean up contributing --- contributing/index.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/contributing/index.md b/contributing/index.md index 9c2f904a..bf8934d7 100644 --- a/contributing/index.md +++ b/contributing/index.md @@ -2,5 +2,5 @@ ## Minor changes or clarifications -Minor changes or clarifications to the specification should be made against the copy in the `latest` folder. -Please add a changelog entry explaining clearly the change you are making, so when a new version of the specifciation is released it is clear what has changed. +Minor changes or clarifications to the specification can be made by opening a pull request with changes made against against the copy in the `latest` folder. +Please add a changelog entry explaining clearly the change you are making.