ome · lubianat · Jun 4, 2026 · Jun 4, 2026 · Jun 4, 2026 · Jun 4, 2026
diff --git a/boilerplate/copyright.include b/boilerplate/copyright.include
@@ -0,0 +1,4 @@
+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.
diff --git a/boilerplate/header.include b/boilerplate/header.include
@@ -0,0 +1,31 @@
+<!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">
+
+  <img src="http://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/conf.py b/conf.py
@@ -17,15 +17,12 @@
     "myst_parser",
     "sphinx_reredirects",
     "sphinx_design",
-    "sphinxcontrib.bibtex"]
+    "sphinxcontrib.bibtex",
+]
 bibtex_bibfiles = ["references.bib"]
 source_suffix = [".rst", ".md"]
 myst_heading_anchors = 5
-myst_enable_extensions = [
-    "deflist",
-    "strikethrough",
-    "colon_fence"
-    ]
+myst_enable_extensions = ["deflist", "strikethrough", "colon_fence"]
 
 templates_path = ["_templates"]
 exclude_patterns = [
@@ -57,7 +54,7 @@
     "latest/index": "../specifications/0.5/index.html",
     "latest/": "../specifications/0.5/index.html",
     "dev/index": "../specifications/dev/index.html",
-    "dev/": "../specifications/dev/index.html"
+    "dev/": "../specifications/dev/index.html",
 }
 
 # -- Options for HTML output -------------------------------------------------
@@ -78,6 +75,8 @@
     "use_download_button": True,
 }
 
+html_favicon = "images/favicon-16x16.png"
+
 html_static_path = ["_static"]
 
 html_css_files = [
@@ -93,6 +92,7 @@
     "_html_extra",
 ]
 
+
 def build_served_html():
     import glob
     import subprocess
@@ -102,34 +102,58 @@ def build_served_html():
     from pathlib import Path
 
     os.chdir(Path(__file__).parent)
-    versions = [d for d in os.listdir("specifications") if os.path.isdir(os.path.join("specifications", d))]
+    versions = [
+        d
+        for d in os.listdir("specifications")
+        if os.path.isdir(os.path.join("specifications", d))
+    ]
 
     for version in versions:
 
         # copy schemas to _html_extra
-        os.makedirs(f'_html_extra/{version}/schemas', exist_ok=True)
-        schemas = glob.glob(f'specifications/{version}/**/*.schema', recursive=True)
+        os.makedirs(f"_html_extra/{version}/schemas", exist_ok=True)
+        schemas = glob.glob(f"specifications/{version}/**/*.schema", recursive=True)
         for schema in schemas:
-            shutil.copy2(schema, f'_html_extra/{version}/schemas/')
-        print(f'✅ Copied schemas for version {version}')
-    
+            shutil.copy2(schema, f"_html_extra/{version}/schemas/")
+        print(f"✅ Copied schemas for version {version}")
+
         # find 'pre_build.py' in 'specifications' subdirectories
-        script = glob.glob(f'specifications/{version}/**/pre_build.py', recursive=True)[0]
+        script = glob.glob(f"specifications/{version}/**/pre_build.py", recursive=True)[
+            0
+        ]
+
+        # Inject shared OME boilerplate next to index.bs so the legacy Bikeshed
+        # build renders OME branding instead of falling back to the W3C default.
+        # Kept here in the superproject so we never have to edit, commit, and
+        # bump every ngff-spec version submodule (the includes were lost exactly
+        # that way during the ngff -> ngff-spec migration).
+        spec_dir = os.path.dirname(script)
+        for inc in ("header.include", "copyright.include"):
+            src = os.path.join("boilerplate", inc)
+            if os.path.exists(src):
+                shutil.copy2(src, os.path.join(spec_dir, inc))
+                print(f"✅ Injected {inc} for version {version}")
+            else:
+                print(
+                    f"⚠️  Missing boilerplate/{inc}; {version} will use Bikeshed defaults"
+                )
 
         subprocess.check_call([sys.executable, script])
-        print('✅ Built rendered examples/schemas for version', version)
+        print("✅ Built rendered examples/schemas for version", version)
 
         # build jupyter-book docs in specification submodules
-        myst_file = glob.glob(f'specifications/{version}/**/myst.yml', recursive=True)[0]
-        bikeshed_output = f'specifications/{version}/index.html'
+        myst_file = glob.glob(f"specifications/{version}/**/myst.yml", recursive=True)[
+            0
+        ]
+        bikeshed_output = f"specifications/{version}/index.html"
 
         # copy built html files to _html_extra
         try:
             if os.path.exists(bikeshed_output):
-                shutil.copy2(bikeshed_output, f'_html_extra/{version}/index.html')
-                print(f'✅ Found legacy bikeshed, serving as extra html for {version}')
+                shutil.copy2(bikeshed_output, f"_html_extra/{version}/index.html")
+                print(f"✅ Found legacy bikeshed, serving as extra html for {version}")
         except Exception as e:
-            print(f'⚠️  Could not copy served html for version {version}: {e}')
+            print(f"⚠️  Could not copy served html for version {version}: {e}")
+
 
 build_served_html()
-
diff --git a/images/favicon-16x16.png b/images/favicon-16x16.png
diff --git a/readthedocs.yml b/readthedocs.yml
@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-24.04
   tools:
-    python: "3.10"
+    python: "3.13"
     nodejs: "22"
 
 submodules:
@@ -21,4 +21,4 @@ python:
   install:
     - requirements: requirements.txt
     - method: pip
-      path: specifications/dev
+      path: specifications/dev
diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
-bikeshed<4.2
+bikeshed
 myst-parser
 pydata-sphinx-theme
 json-schema-for-humans

diff --git a/resources/data/index.md b/resources/data/index.md
@@ -1,27 +1,71 @@
-Data Resources
-==============
-
-| Catalog                                                                  | Hosting                                              | Zarr Files   | Size     |
-| ------------------------------------------------------------------------ | -----------------------------------------------------| ------------ | -------- |
-| [BIA Samples](https://bit.ly/bia-ome-ngff-samples)                       | EBI                                                  | 90           | 200 GB   |
-| [BioFile Finder](https://bff.allencell.org/datasets)                     | AWS Open Data Program & others                       | 78091        | ? TB     |
-| [CryoET Data Portal](https://cryoetdataportal.czscience.com)             | AWS Open Data Program                                | 37585        | 70 TB    |
-| [Cell Painting Gallery](https://github.com/broadinstitute/cellpainting-gallery) | AWS Open Data Program                         | 136          | 20 TB    |
-| [CZB-Zebrahub](https://zebrahub.ds.czbiohub.org/imaging)                 | czbiohub                                             | 5            | 1.2 TB   |
-| [DANDI](https://dandiarchive.org/dandiset/000108) ([identifiers.org][dandi2],[github][dandi3]) | AWS Open Data Program          | 3914         | 355 TB   |
-| [JAX](https://images.jax.org/webclient/userdata/?experimenter=-1)        | The Jackson Laboratory                               | 17000        | 192 TB   |
-| [Glencoe](https://glencoesoftware.com/ngff)                              | Glencoe Software, Inc.                               | 8            | 165 GB   |
-| [IDR Samples](https://idr.github.io/ome-ngff-samples/)                   | EBI                                                  | 88           | 3 TB     |
-| [IDR Studies](https://livingobjects.ebi.ac.uk/bioimaging-integrator-data/pages/idr_ngff_data.html) | EBI                               | 1644         | 47 TB    |
-| [MoBIE](https://mobie.github.io/specs/ngff.html)                         | EMBL-HD                                              | 21           | 2 TB     |
-| [Neural Dynamics](https://registry.opendata.aws/allen-nd-open-data/)     | AWS Open Data Program                                | 90           | 200 TB   |
-| [Open SciVis](https://registry.opendata.aws/ome-zarr-open-scivis/)       | AWS Open Data Program                                | 624          | 372 GB   |
-| [Sanger](https://www.sanger.ac.uk/project/ome-zarr/)                     | Sanger, UK                                           | 10           | 1 TB     |
-| [SpatialData](https://github.com/scverse/spatialdata-notebooks/tree/main/datasets)                       | EMBL-HD              | 10           | 25 GB    |
-| [SSBD](https://ssbd.riken.jp/ssbd-ome-ngff-samples)                      | SSBD                                                 | 5000         | 20 TB    |
-| [webKnossos](https://zarr.webknossos.org)                                | scalable minds                                       | 69           | 70 TB    |
-
-OME-Zarr 0.5 data has been collected during [the OME 2024 NGFF challenge](https://ome.github.io/ome2024-ngff-challenge/).
-
-[dandi2]: https://identifiers.org/DANDI:000108
-[dandi3]: https://github.com/dandisets/000108
+# Data Resources
+
+Looking for test data? [IDR Samples](https://idr.github.io/ome-ngff-samples/) aims at covering the different corners of the specification.
+
+After this quick reference, you can find a diverse set of data resources in OME-Zarr format, illustrating the range of scientific stories enabled by the format.
+
+Do you have a data resource in OME-Zarr format that you would like to share? Is there something missing? Please submit an [issue](https://github.com/ome/ngff/issues) or [pull request](https://github.com/ome/ngff/pulls) to update this list.
+
+## Sample data
+
+Resources curating OME-Zarr sample data, for demonstration and testing purposes.
+
+| Resource   | Description      |
+| ---- | ---------------------- |
+| [IDR Samples](https://idr.github.io/ome-ngff-samples/)                                | A comprehensive set of OME-Zarr samples from IDR, covering all OME-Zarr versions                                                |
+| [BIA Samples](https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/omengff.html) | Sample OME-Zarr datasets from the BioImage Archive for testing                                                                  |
+| [Sanger Institute Samples ](https://www.sanger.ac.uk/project/ome-zarr/)               | Datasets from the Sanger Institute that have been converted to OME-Zarr to test and encourage the file format                   |
+| [SSBD samples](https://ssbd.riken.jp/ssbd-ome-ngff-samples)                           | Sample OME-Zarr datasets from the Systems Science of Biological Dynamics database (SSBD) for testing and demonstration purposes |
+| [OME 2024 NGFF challenge](https://ome.github.io/)              | Close to 500 TB of data in the OME-Zarr 0.5 format                                                                              |
+
+## Data portals
+
+Imaging data portals with curated OME-Zarr data, including public repositories. The content in the repositories may grow with time as new datasets become available.
+
+| Resource   | Description      |
+| ---- | ---------------------- |
+| [CryoET Data Portal](https://cryoetdataportal.czscience.com)                                       | Cryo-electron tomography (cryoET) data repository                                                                                                  |
+| [BioFile Finder](https://bff.allencell.org/datasets)                                               | A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support                                   |
+| [JAX OMERO](https://images.jax.org/webclient/userdata/?experimenter=-1)                            | The Jackson Laboratory public OMERO instance, links to OME-Zarr files are available in the key-value                                               |
+| [webknossos Zarr Gallery](https://zarr.webknossos.org)                                             | A collection of mostly Electron Microscopy OME-Zarr datasets from webKnossos, a platform for large-scale 3D image data visualization and analysis. |
+| [IDR Studies](https://livingobjects.ebi.ac.uk/bioimaging-integrator-data/pages/idr_ngff_data.html) | A collection of OME-Zarr datasets from the Image Data Resource (IDR), a public repository for bioimaging data                                      |
+
+## Datasets
+
+These are datasets available in OME-Zarr format, hosted in various locations. They represent some of the different scientific stories enabled by OME-Zarr.
+
+| Resource   | Description      |
+| ---- | ---------------------- |
+| [Open SciVis](https://registry.opendata.aws/ome-zarr-open-scivis/) [source](https://github.com/InsightSoftwareConsortium/OMEZarrOpenSciVisDatasets) | A collection of of volumetric datasets in OME-Zarr format, including several CT scans. |
+| [Herculaneum Scrolls](https://registry.opendata.aws/vesuvius-challenge-herculaneum-scrolls/) [source](https://github.com/ScrollPrize/open-data)| Scrolls carbonized by Mount Vesuvius eruptions imaged via X-ray micro-CT, made available in OME-Zarr format.|
+| [VoDaSuRe](https://augusthoeg.github.io/VoDaSuRe/)| A large-scale dataset covering volumetric super-resolution data with micro-CT ([arXiv](https://arxiv.org/abs/2603.23153); [dataset](https://huggingface.co/datasets/AugustHoeg/VoDaSuRe))|
+
+## Atlases
+
+These are "atlas"-like datasets, which provide a comprehensive view of a particular biological system. The metadata-rich, streaming-friendly nature of OME-Zarr makes it ideal for sharing and visualizing large, complex datasets that are often associated with atlases.
+
+The [WebAtlas pipeline](https://cellatlas.io/webatlas) ([Li et al, 2024](https://www.nature.com/articles/s41592-024-02371-x)) demonstrates how OME-Zarr can be used in the context of deploying such atlases in the context of spatial transcriptomics. The examples, however, cover also other types of data, including volumetric electron microscopy, expansion microscopy and light sheet imaging.
+
+##
+
+| Resource    | Description       | Publication          | Sample      |
+| ----------- | ----------------- | -------------------- | ----------- |
+| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging)   | Multimodal atlas of zebrafish development including light-sheet imaging | [Lange et al., 2024](https://doi.org/https://doi.org/10.1016/j.cell.2024.09.047)      | [zebrahub](https://zebrahub.sf.czbiohub.org/ngv?name=ZMNS001)      |
+| [ExÂME: Expansion Microscopy Atlas of Microbial Eukayotes](https://www.dudinlab.com/exame) (see also [S-BIAD2095](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2095)) | An atlas of expansion microscopy images of microbial eukaryotes, including OME-Zarr datasets ([highlight](https://www.nature.com/immersive/d41586-026-00901-5/index.html)) | [Mikus et al., 2024](https://doi.org/10.1101/2024.10.18.618984)                                                                         | [vizarr](https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/vizarr/index.html?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2095/d39625f2-590d-4e19-9f61-37489318b1c0/3c55c404-49e4-4e9d-bb76-c028b08835d3.ome.zarr/0)|
+| [The Human Organ Atlas](https://human-organ-atlas.esrf.fr/)               | Atlas of organs using  Hierarchical Phase-Contrast Tomography (HiP-CT)       | [Walsh et al., 2026](https://www.science.org/doi/10.1126/sciadv.adz2240)                                                                                     | [Human Organ Atlas](https://human-organ-atlas.esrf.fr/datasets/2439291070) |
+| [The Genetic Tools Atlas](https://brain-map.org/bkp/experiment/genetic-tools/genetic-tools-atlas)    | A searchable web tool representing information and data on enhancer-adeno-associated viruses (enhancer AAVs) and mouse transgenes    | [Ben-Simon et al., 2025](<https://www.cell.com/cell/fulltext/S0092-8674(25)00513-6>) | [atlas](https://knowledge.brain-map.org/data/7CVKSF7QGAKIQ8LM5LC/specimens/3PILF5KFKGJILDK30H2)
+| [Platynereis cell atlas](https://platynereis.com/resources/image/)                                                                                                                | An expression atlas registered to a whole-body electron microscopy volume of the nereid *Platynereis dumerilii* | [Vergara et al., 2021](https://doi.org/10.1016/j.cell.2021.07.017)                   | [neuroglancer](https://tiago.bio.br/links?go=platy-atlas)                                                                                                                                                                            |
+| [OpenOrganelle](https://openorganelle.janelia.org/)                                                                                                                               | An open-access volume electron microscopy atlas of whole cells and tissues                                                                                                   | [Xu et al., 2021](https://www.nature.com/articles/s41586-021-03992-4)                | [neuroglancer](https://tiago.bio.br/links?go=open-organelle)                                                                                                                                                                         |
+
+---
+
+# Other resources
+
+These are resources that may not be exclusively OME-Zarr, but include some OME-Zarr data that may be of interest to the community.
+
+| Resource   | Description      |
+| ---- | ---------------------- |
+| [DANDI](https://dandiarchive.org/), e.g. [000108](https://dandiarchive.org/dandiset/000108)                                                           | BRAIN Initiative archive for publishing and sharing neurophysiology data                                                   |
+| [Cell Painting Gallery](https://broadinstitute.github.io/cellpainting-gallery), e.g. [cpg0004-lincs](https://idr.github.io/idr0125-way-cellpainting/) | A collection of datasets from the Cell Painting assay, a high-content image-based assay for profiling cellular phenotypes. |
+| [AIND - Mouse Neuroanatomy and Physiology Data](https://registry.opendata.aws/allen-nd-open-data/)                                                    | Datasets from the Allen Institute for Neural Dynamics, including OME-Zarr.                                                 |
+| [SpatialData datasets](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html)                                            | A collection of spatial omics datasets using the SpatialData specification, which includes OME-Zarr.                       |