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Add instructions on how to contribute a minor change #281

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Add instructions on how to contribute a minor change #281

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c30bd4d
Populate latest folder with copy of spec
dstansby Nov 29, 2024
9ed7f06
Add contributing + changelog guidelines
dstansby Nov 29, 2024
1e2e5b4
Add contributing to ToC
dstansby Nov 29, 2024
befc8da
Clean up contributing
dstansby Nov 29, 2024
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6 changes: 6 additions & 0 deletions contributing/index.md
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# Contributing

## Minor changes or clarifications

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.
1 change: 1 addition & 0 deletions index.rst
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Expand Up @@ -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
Expand Down
1 change: 0 additions & 1 deletion latest
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This file was deleted.

4 changes: 4 additions & 0 deletions latest/copyright.include
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Copyright © 2020-[YEAR]
<a href="https://www.openmicroscopy.org/"><abbr title="Open Microscopy Environment">OME</abbr></a><sup>®</sup>
(<a href="https://dundee.ac.uk/"><abbr title="University of Dundee">U. Dundee</abbr></a>).
OME trademark rules apply.
3 changes: 3 additions & 0 deletions latest/examples/bf2raw/.config.json
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{
"schema": "schemas/bf2raw.schema"
}
10 changes: 10 additions & 0 deletions latest/examples/bf2raw/image.json
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{
"zarr_format": 3,
"node_type": "group",
"attributes": {
"ome": {
"version": "0.5",
"bioformats2raw.layout": 3
}
}
}
36 changes: 36 additions & 0 deletions latest/examples/bf2raw/plate.json
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{
"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
}
]
}
}
}
}
3 changes: 3 additions & 0 deletions latest/examples/label_strict/.config.json
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{
"schema": "schemas/strict_label.schema"
}
37 changes: 37 additions & 0 deletions latest/examples/label_strict/colors_properties.json
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{
"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": "../../"
}
}
}
}
}
3 changes: 3 additions & 0 deletions latest/examples/multiscales_strict/.config.json
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{
"schema": "schemas/strict_image.schema"
}
68 changes: 68 additions & 0 deletions latest/examples/multiscales_strict/multiscales_example.json
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{
"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 }
}
}
]
}
}
}
47 changes: 47 additions & 0 deletions latest/examples/multiscales_strict/multiscales_transformations.json
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{
"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"
}
}
]
}
}
}
3 changes: 3 additions & 0 deletions latest/examples/ome/.config.json
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{
"schema": "schemas/ome.schema"
}
10 changes: 10 additions & 0 deletions latest/examples/ome/series-2.json
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{
"zarr_format": 3,
"node_type": "group",
"attributes": {
"ome": {
"version": "0.5",
"series": ["0", "1"]
}
}
}
3 changes: 3 additions & 0 deletions latest/examples/plate_strict/.config.json
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{
"schema": "schemas/strict_plate.schema"
}
97 changes: 97 additions & 0 deletions latest/examples/plate_strict/plate_2wells.json
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{
"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
}
]
}
}
}
}
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