ome · joshmoore · Apr 21, 2023 · Mar 14, 2023 · Mar 14, 2023 · Mar 14, 2023
diff --git a/.gitignore b/.gitignore
@@ -1,2 +1,6 @@
 */.DS_Store
-**/__pycache__/*
+**/__pycache__/*
+*/index.html
+_build
+_bikeshed
+.tox
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,8 @@
+version: 2
+
+sphinx:
+  configuration: conf.py
+
+python:
+  install:
+    - requirements: requirements.txt
diff --git a/0.1/index.bs b/0.1/index.bs
@@ -501,8 +501,7 @@ Projects which support reading and/or writing OME-NGFF data include:
 
 </dl>
 
-<img src="https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/images/zarr-ome-diagram.png"
-    alt="Diagram of related projects"/>
+<img src="https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/images/zarr-ome-diagram.png" alt="Diagram of related projects"></img>
 
 All implementations prevent an equivalent representation of a dataset which can be downloaded or uploaded freely. An interactive
 version of this diagram is available from the [OME2020 Workshop](https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/).

diff --git a/0.2/index.bs b/0.2/index.bs
@@ -559,8 +559,7 @@ Projects which support reading and/or writing OME-NGFF data include:
 
 </dl>
 
-<img src="https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/images/zarr-ome-diagram.png"
-    alt="Diagram of related projects"/>
+<img src="https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/images/zarr-ome-diagram.png" alt="Diagram of related projects"></img>
 
 All implementations prevent an equivalent representation of a dataset which can be downloaded or uploaded freely. An interactive
 version of this diagram is available from the [OME2020 Workshop](https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/).

diff --git a/0.3/index.bs b/0.3/index.bs
@@ -569,8 +569,7 @@ Projects which support reading and/or writing OME-NGFF data include:
 
 </dl>
 
-<img src="https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/images/zarr-ome-diagram.png"
-    alt="Diagram of related projects"/>
+<img src="https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/images/zarr-ome-diagram.png" alt="Diagram of related projects"></img>
 
 All implementations prevent an equivalent representation of a dataset which can be downloaded or uploaded freely. An interactive
 version of this diagram is available from the [OME2020 Workshop](https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/).

diff --git a/0.4/index.bs b/0.4/index.bs
@@ -639,8 +639,7 @@ Projects which support reading and/or writing OME-NGFF data include:
 
 </dl>
 
-<img src="https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/images/zarr-ome-diagram.png"
-    alt="Diagram of related projects"/>
+<img src="https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/images/zarr-ome-diagram.png" alt="Diagram of related projects"></img>
 
 All implementations prevent an equivalent representation of a dataset which can be downloaded or uploaded freely. An interactive
 version of this diagram is available from the [OME2020 Workshop](https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/).

diff --git a/Makefile b/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/about/index.md b/about/index.md
@@ -0,0 +1,26 @@
+About
+=====
+
+In addition to the next-generation file format (NGFF) [specifications](../specifications/index.md),
+the pages listed below are intended to provide an overview of external resources available
+for working with NGFF data.
+
+The following pages are intended to provide an overview of the available resources in the NGFF space:
+
+* [Data Resources](../data/index.md): List of data repositories where OME-Zarr data can be found.
+* [Tools](../tools/index.rst): GUIs and libraries that can be used for accessing OME-Zarr formatted data.
+* [Publications](../publications/index.md): List of publications referencing OME-NGFF or publishing
+  datasets in OME-Zarr.
+
+Additionally, notes and recordings of the passt NGFF community calls are available:
+
+| Call | Date | Presenters | Forum thread | Notes |
+|------|------|------------|--------------|-------|
+|1| 2020-10-20 | | [image.sc](https://forum.image.sc/t/upcoming-calls-on-next-gen-bioimaging-data-tools-starting-oct-29/43489) | [hackmd](https://hackmd.io/_sftykiGR9mSyUan3l1WmA) |
+|2| 2020-12-02 (with I2K)| | [image.sc](https://forum.image.sc/t/next-call-on-next-gen-bioimaging-data-tools-dec-2/45816) | [hackmd](https://hackmd.io/X348vzCaTRSmIpsa3dK-Sg)|
+|3| 2021-02-23| |[image.sc](https://forum.image.sc/t/next-call-on-next-gen-bioimaging-data-tools-feb-23/48386)| [hackmd](https://hackmd.io/Ndb5IHRmQn2PCCNBLkG-fQ)|
+|4| 2021-06 with Fiji Hackathon| |[image.sc](https://forum.image.sc/t/fiji-hackathon-2021-big-data-days-a/53926)| | |
+|5 (0.4/axes)| 2021-09-02|  Constantin | [image.sc](https://forum.image.sc/t/next-call-on-next-gen-bioimaging-data-tools-feb-23/48386) | [hackmd](https://hackmd.io/GZ1euZUSRZeqPTJj9WJEtg)|
+|6 (0.4/axes)| 2022-01-27| Constantin, Will, Seb| [image.sc](https://forum.image.sc/t/next-call-on-next-gen-bioimaging-data-tools-2022-01-27/60885)| [hackmd](https://hackmd.io/QfiBKHIoTZ-CJSp3q0Wykg)|
+|7 (0.5/tables & transforms)| 2022-10-05| Kevin & John| [image.sc](https://forum.image.sc/t/ome-ngff-community-call-transforms-and-tables/71792)| [hackmd](https://hackmd.io/TyfrLiCqRteL0Xfc8HRiOA) |
+|8 (Metadata) | 2023-03-15 | Wouter-Michiel | [image.sc](https://forum.image.sc/t/community-call-metadata-in-ome-ngff/77570/10) | [hackmd](https://hackmd.io/BqnK9Wm4QpGYAhYOoaFBQQ) |
diff --git a/conf.py b/conf.py
@@ -0,0 +1,79 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'NGFF'
+copyright = '2023, NGFF Community'
+author = 'NGFF Community'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = ["myst_parser"]
+source_suffix = [".rst", ".md"]
+
+templates_path = ['_templates']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '.git', '.pytest_cache', '**/.pytest_cache', '**/.tox', 'README.md', 'LICENSE.md', 'CONTRIBUTING.md']
+
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'sphinx_book_theme'
+
+html_static_path = ['_static']
+
+html_css_files = [
+    'https://cdn.datatables.net/v/dt/dt-1.11.5/datatables.min.css',
+]
+
+html_js_files = [
+    'https://cdn.datatables.net/v/dt/dt-1.11.5/datatables.min.js',
+    'main.js',
+]
+
+html_extra_path = [
+    '_bikeshed',
+]
+
+# ####################################
+# Run bikeshed build
+# ####################################
+
+def bikeshed():
+
+    import glob
+    import os
+    import shutil
+    import subprocess
+
+    for index_file in ["latest/index.bs"] + glob.glob("[0-9]*/index.bs"):
+
+        output_file = index_file.replace("bs", "html")
+        output_dir = os.path.dirname(output_file)
+        target_dir = os.path.join("_bikeshed", output_dir)
+
+        run_bikeshed = True
+
+        # Give the loop a chance to skip files if no build is needed/requested
+        if "BIKESHED" not in os.environ and os.path.exists(output_file):
+            src_time = os.path.getmtime(index_file)
+            out_time = os.path.getmtime(output_file)
+            if src_time < out_time:
+                print(f"{index_file} unchanged")
+                run_bikeshed = False
+
+        if run_bikeshed:
+            subprocess.check_call(f"bikeshed  spec {index_file} {output_file}", shell=True)
+
+        if os.path.exists(target_dir):
+            shutil.rmtree(target_dir)
+        shutil.copytree(output_dir, target_dir)
+
+bikeshed()
+del bikeshed
diff --git a/data/index.html b/data/index.html
diff --git a/data/index.md b/data/index.md
@@ -0,0 +1,16 @@
+Data Resources
+==============
+
+| Catalog                                                                  | Descriptions                                                                                                        | Zarr Files   | Size    |
+| ------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------- | ------------ | ------- |
+| [BIA Samples](https://bit.ly/bia-ome-ngff-samples)                       | Hosting provided by EBI                                                                                             | 90           | 200GB   |
+| [Glencoe](https://glencoesoftware.com/ngff)                              | Hosting provided by Glencoe Software, Inc.                                                                          | TBD          | TBD     |
+| [DANDI](https://dandiarchive.org/dandiset/000108) ([identifiers.org][dandi2],[github][dandi3]) | Hosting provided by AWS Open Data Program                                                                           | 3914         | 355TB   |
+| [EMBL-HD](https://mobie.github.io/specs/ngff.html)                       | Hosting provided by EMBL                                                                                            | 21           | TBD     |
+| [IDR Samples](https://idr.github.io/ome-ngff-samples/)                   | Hosting provided by EBI                                                                                             | 88           | 3TB     |
+| [Neural Dynamics](https://registry.opendata.aws/allen-nd-open-data/)     | Hosting provided by AWS Open Data Program                                                                           | 90           | 200TB   |
+| [Sanger](https://www.sanger.ac.uk/project/ome-zarr/)                     | Hosting provided by Sanger, UK                                                                                      | 10           | 1TB     |
+| [webKnossos](https://zarr.webknossos.org)                                | Hosting provided by scalableminds GmbH                                                                              | 69           | 70TB    |
+
+[dandi2]: https://identifiers.org/DANDI:000108
+[dandi3]: https://github.com/dandisets/000108
diff --git a/index.html b/index.html
diff --git a/index.rst b/index.rst
@@ -0,0 +1,25 @@
+.. NGFF documentation master file, created by
+   sphinx-quickstart on Tue Mar 14 08:54:12 2023.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Next-generation file formats (NGFF)
+===================================
+
+.. toctree::
+   :maxdepth: 2
+
+   about/index
+   data/index
+   specifications/index
+   tools/index
+
+..
+   # Temporarily disabled
+   publications/index
+
+.. raw:: html
+
+    <script type="text/javascript">
+        window.location.replace('latest/index.html');
+    </script>
diff --git a/latest/index.bs b/latest/index.bs
@@ -648,8 +648,7 @@ Projects which support reading and/or writing OME-NGFF data include:
 
 </dl>
 
-<img src="https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/images/zarr-ome-diagram.png"
-    alt="Diagram of related projects"/>
+<img src="https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/images/zarr-ome-diagram.png" alt="Diagram of related projects"></img>
 
 All implementations prevent an equivalent representation of a dataset which can be downloaded or uploaded freely. An interactive
 version of this diagram is available from the [OME2020 Workshop](https://downloads.openmicroscopy.org/presentations/2020/Dundee/Workshops/NGFF/zarr_diagram/).

diff --git a/make.bat b/make.bat
@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd
diff --git a/publications/index.md b/publications/index.md
@@ -0,0 +1,7 @@
+Publications
+============
+
+* OME-NGFF
+* OME-Zarr
+* vEM
+* Talks? Videos
diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,3 @@
+bikeshed
+myst-parser
+sphinx-book-theme
diff --git a/specifications/index.md b/specifications/index.md
@@ -0,0 +1,12 @@
+Specifications
+==============
+
+<ul>
+  <li> <a href="../0.1/index.html">0.1</a> </li>
+  <li> <a href="../0.2/index.html">0.2</a> </li>
+  <li> <a href="../0.3/index.html">0.3</a> </li>
+  <li> <a href="../0.4/index.html">0.4</a> </li>
+  <li> <a href="../latest/index.html">latest</a> </li>
+</ul>
+
+By default <https://ngff.openmicroscopy.org> will redirect to latest
diff --git a/tools/index.html b/tools/index.html
diff --git a/tools/index.md b/tools/index.md
@@ -0,0 +1,76 @@
+# Tools
+
+A list of tools which support OME-Zarr
+
+## Visualization Tools
+
+### AGAVE
+<https://github.com/allen-cell-animated/agave>
+
+
+### ITKWidgets
+<https://github.com/InsightSoftwareConsortium/itkwidgets>
+
+
+### MoBIE/BDV
+<https://github.com/mobie/mobie-viewer-fiji>
+
+
+### napari
+<https://github.com/napari/napari>
+
+
+### Neuroglancer
+<https://github.com/google/neuroglancer>
+
+
+### Viv
+<https://github.com/hms-dbmi/viv>
+
+<iframe style="width: 100%; height: 500px" name="vizarr" src="https://hms-dbmi.github.io/vizarr/v0.1/?source=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/4495402.zarr">
+</iframe>
+
+
+### webKnossos
+<https://github.com/scalableminds/webknossos>
+
+
+### website-3d-cell-viewer
+<https://github.com/allen-cell-animated/website-3d-cell-viewer>
+
+
+## Utilities
+
+### bioformats2raw
+<https://github.com/glencoesoftware/bioformats2raw>
+
+
+### ome-ngff-validator
+<https://github.com/ome/ome-ngff-validator>
+
+
+### NGFF-Converter
+<https://github.com/glencoesoftware/NGFF-Converter>
+
+
+## Libraries
+
+### aicsimageio
+<https://github.com/AllenCellModeling/aicsimageio>
+
+
+### tensorstore
+<https://github.com/google/tensorstore/>
+
+
+### Fractal
+<https://github.com/fractal-analytics-platform/fractal>
+
+
+### Bio-Formats
+<https://github.com/ome/bioformats>
+
+
+### ome-zarr-py
+<https://github.com/ome/ome-zarr-py>
+