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Merge pull request #242 from normanrz/spec-rfc2
Changes to the spec and schemata for RFC-2
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@@ -14,6 +14,7 @@ jobs: | |
| - '0.2' | ||
| - '0.3' | ||
| - '0.4' | ||
| - '0.5' | ||
| - 'latest' | ||
| runs-on: ubuntu-20.04 | ||
| steps: | ||
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| @@ -1,7 +1,7 @@ | ||
| version: 2 | ||
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| build: | ||
| os: ubuntu-22.04 | ||
| os: ubuntu-24.04 | ||
| tools: | ||
| python: "3.10" | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,34 @@ | ||
| <!DOCTYPE html> | ||
| <html lang="en"> | ||
| <head> | ||
| <meta http-equiv="Content-Type" content="text/html; charset=utf-8"> | ||
| <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> | ||
| <title>[TITLE]</title> | ||
| <style data-fill-with="stylesheet"> | ||
| </style> | ||
| </head> | ||
| <body class="h-entry"> | ||
| <div class="head"> | ||
|
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||
| <!--p data-fill-with="logo"></p--> | ||
| <img src="https://www.openmicroscopy.org/img/logos/ome-logomark.svg" | ||
| alt="OME logo (6 circles in a hexagon)" | ||
| style="float:right;width:42px;height:42px;"> | ||
|
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| <h1 id="title" class="p-name no-ref">[TITLE]</h1> | ||
| <h2 id="subtitle" class="no-num no-toc no-ref">[LONGSTATUS], | ||
| <time class="dt-updated" datetime="[ISODATE]">[DATE]</time></h2> | ||
| <div data-fill-with="spec-metadata"></div> | ||
| <div data-fill-with="warning"></div> | ||
| <p class='copyright' data-fill-with='copyright'></p> | ||
| <hr title="Separator for header"> | ||
| </div> | ||
|
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| <div class="p-summary" data-fill-with="abstract"></div> | ||
|
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| <h2 class='no-num no-toc no-ref' id='sotd'>Status of this document</h2> | ||
| <div data-fill-with="status"></div> | ||
| <div data-fill-with="at-risk"></div> | ||
|
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| <nav data-fill-with="table-of-contents" id="toc"></nav> | ||
| <main> |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| { | ||
| "zarr_format": 3, | ||
| "node_type": "group", | ||
| "attributes": { | ||
| "ome": { | ||
| "version": "0.5", | ||
| "bioformats2raw.layout": 3 | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 | ||
| } | ||
| ] | ||
| } | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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": "../../" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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 } | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| } | ||
| } |
47 changes: 47 additions & 0 deletions
47
0.5/examples/multiscales_strict/multiscales_transformations.json
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|---|---|---|
| @@ -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" | ||
| } | ||
| } | ||
| ] | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| { | ||
| "zarr_format": 3, | ||
| "node_type": "group", | ||
| "attributes": { | ||
| "ome": { | ||
| "version": "0.5", | ||
| "series": ["0", "1"] | ||
| } | ||
| } | ||
| } |
File renamed without changes.
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