ome · joshmoore · Nov 22, 2024 · May 30, 2024 · Jun 2, 2024 · Jun 28, 2024
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -12,7 +12,7 @@ on:
 jobs:
   main:
     name: Build, Validate and Deploy
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/checkout@v2
       - uses: ome/spec-prod@main

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
@@ -14,6 +14,7 @@ jobs:
           - '0.2'
           - '0.3'
           - '0.4'
+          - '0.5'
           - 'latest'
     runs-on: ubuntu-20.04
     steps:

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -1,7 +1,7 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
     python: "3.10"
 

diff --git a/0.1/index.bs b/0.1/index.bs
@@ -3,13 +3,12 @@ Title: Next-generation file formats (NGFF)
 Shortname: ome-ngff
 Level: 1
 Status: w3c/CG-FINAL
-Group: ome
+TR: https://ngff.openmicroscopy.org/0.1/
 URL: https://ngff.openmicroscopy.org/0.1/
 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
-Local Boilerplate: copyright yes
+Local Boilerplate: header yes, copyright yes
 Boilerplate: style-darkmode off
 Markup Shorthands: markdown yes
 Editor: Josh Moore, Open Microscopy Environment (OME) https://www.openmicroscopy.org

diff --git a/0.2/index.bs b/0.2/index.bs
@@ -3,13 +3,12 @@ Title: Next-generation file formats (NGFF)
 Shortname: ome-ngff
 Level: 1
 Status: w3c/CG-FINAL
-Group: ome
+TR: https://ngff.openmicroscopy.org/0.2/
 URL: https://ngff.openmicroscopy.org/0.2/
 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
-Local Boilerplate: copyright yes
+Local Boilerplate: header yes, copyright yes
 Boilerplate: style-darkmode off
 Markup Shorthands: markdown yes
 Editor: Josh Moore, Open Microscopy Environment (OME) https://www.openmicroscopy.org

diff --git a/latest/header.include → 0.3/header.include b/latest/header.include → 0.3/header.include
diff --git a/0.3/index.bs b/0.3/index.bs
@@ -3,13 +3,12 @@ Title: Next-generation file formats (NGFF)
 Shortname: ome-ngff
 Level: 1
 Status: w3c/CG-FINAL
-Group: ome
+TR: https://ngff.openmicroscopy.org/0.3/
 URL: https://ngff.openmicroscopy.org/0.3/
 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
-Local Boilerplate: copyright yes
+Local Boilerplate: header yes, copyright yes
 Boilerplate: style-darkmode off
 Markup Shorthands: markdown yes
 Editor: Josh Moore, Open Microscopy Environment (OME) https://www.openmicroscopy.org

diff --git a/0.4/header.include b/0.4/header.include
@@ -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">
+
+  <!--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;">
+
+  <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>
+
+<div class="p-summary" data-fill-with="abstract"></div>
+
+<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>
+
+<nav data-fill-with="table-of-contents" id="toc"></nav>
+<main>
diff --git a/0.4/index.bs b/0.4/index.bs
@@ -2,15 +2,13 @@
 Title: Next-generation file formats (NGFF)
 Shortname: ome-ngff
 Level: 1
-Status: LS-COMMIT
 Status: w3c/CG-FINAL
-Group: ome
+TR: https://ngff.openmicroscopy.org/0.4/
 URL: https://ngff.openmicroscopy.org/0.4/
 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
-Local Boilerplate: copyright yes
+Local Boilerplate: header yes, copyright yes
 Boilerplate: style-darkmode off
 Markup Shorthands: markdown yes
 Editor: Josh Moore, University of Dundee (UoD) https://www.dundee.ac.uk, https://orcid.org/0000-0003-4028-811X
@@ -241,7 +239,7 @@ keys as specified below for discovering certain types of data, especially images
 
 "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 values for custom axis types that are not part of this specification yet.
+- 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'

diff --git a/latest/copyright.include → 0.5/copyright.include b/latest/copyright.include → 0.5/copyright.include
diff --git a/latest/examples/bf2raw/.config.json → 0.5/examples/bf2raw/.config.json b/latest/examples/bf2raw/.config.json → 0.5/examples/bf2raw/.config.json
diff --git a/0.5/examples/bf2raw/image.json b/0.5/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/0.5/examples/bf2raw/plate.json b/0.5/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 → 0.5/examples/label_strict/.config.json b/latest/examples/label_strict/.config.json → 0.5/examples/label_strict/.config.json
diff --git a/0.5/examples/label_strict/colors_properties.json b/0.5/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/.../examples/multiscales_strict/.config.json → 0.5/examples/multiscales_strict/.config.json b/.../examples/multiscales_strict/.config.json → 0.5/examples/multiscales_strict/.config.json
diff --git a/0.5/examples/multiscales_strict/multiscales_example.json b/0.5/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/0.5/examples/multiscales_strict/multiscales_transformations.json b/0.5/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 → 0.5/examples/ome/.config.json b/latest/examples/ome/.config.json → 0.5/examples/ome/.config.json
diff --git a/0.5/examples/ome/series-2.json b/0.5/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 → 0.5/examples/plate_strict/.config.json b/latest/examples/plate_strict/.config.json → 0.5/examples/plate_strict/.config.json