From 00151232c6070c41922dbec3a53c7bd428c11996 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Fri, 15 May 2026 12:10:58 -0500 Subject: [PATCH 1/4] doc: Add BIDS support for OME-Zarr --- help-desk/index.md | 4 +++- index.md | 2 ++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/help-desk/index.md b/help-desk/index.md index cadbd2ac6..c3d79ff80 100644 --- a/help-desk/index.md +++ b/help-desk/index.md @@ -19,6 +19,8 @@ Jump to: ### B +**BIDS** - Brain Imaging Data Structure (BIDS) is a community-developed standard for organizing and describing neuroscientific data. The [BIDS specification supports OME-Zarr](https://bids-specification.readthedocs.io/en/stable/common-principles.html#imaging-files) as a storage format for imaging data. + [Back to top](#glossary) ### C @@ -143,7 +145,7 @@ As with any initiative involving community consensus, feature adoption and scope **7. Does this format work for non-microscopy data too?** -OME-Zarrs are, by definition, Zarr files with added structures defined by the OME community. These structures have been defined and developed to attend to the needs of the microscopy community, but are by no means limited to those. If you work on other kinds of large multidimensional arrays and you find the OME-Zarr metadata structures useful for your work, great! You might also need different kinds of structures; if you believe these would also be useful for a broader community, engaging with the RFC process is always welcome; otherwise, you might want to consider "pure" Zarr. +OME-Zarrs are, by definition, Zarr files with added structures defined by the OME community. These structures have been defined and developed to attend to the needs of the microscopy community, but are by no means limited to those. If you work on other kinds of large multidimensional arrays and you find the OME-Zarr metadata structures useful for your work, great! For example, the [BIDS specification supports OME-Zarr](https://bids-specification.readthedocs.io/en/stable/common-principles.html#imaging-files) as a storage format for all imaging data. You might also need different kinds of structures; if you believe these would also be useful for a broader community, engaging with the RFC process is always welcome; otherwise, you might want to consider "pure" Zarr. **8. Is OME-Zarr a stable format?** diff --git a/index.md b/index.md index c872cbf0f..2e29bd83d 100644 --- a/index.md +++ b/index.md @@ -51,6 +51,8 @@ These are *some* of the organizations (and their dataset pages) that are using O - [Jackson Laboratory (JAX)](https://images.jax.org/) - ... [and more](/data/index.html) +Additionally, the [BIDS specification supports OME-Zarr](https://bids-specification.readthedocs.io/en/stable/common-principles.html#imaging-files) as a storage format for imaging data. + ## How do I use OME-Zarr? * Already have a Zarr? From d4f87022a60669604fda25a5ed56f0674b14a8e4 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Wed, 9 Sep 2026 05:35:02 -0500 Subject: [PATCH 2/4] Update ecosystem page --- resources/ecosystem/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/ecosystem/index.md b/resources/ecosystem/index.md index 10c92ea10..7497cbf7d 100644 --- a/resources/ecosystem/index.md +++ b/resources/ecosystem/index.md @@ -12,7 +12,7 @@ It fits microscope acquisition software, analysis pipelines, standards and exten | Name | Link | Description | Status | | -------- | ------- | ------- | ------ | | SpatialData | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/scverse/spatialdata) | An open and universal framework for processing spatial omics data. | [published](https://www.nature.com/articles/s41592-024-02212-x) | -| BIDS | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://bids-specification.readthedocs.io/en/stable/common-principles.html#imaging-files) | A community-developed standard for organizing and describing neuroscientific data, currently adding support for OME-Zarr. | [work in progress](https://github.com/bids-standard/bids-specification/pull/2392) | +| BIDS | [![image](https://raw.githubusercontent.com/bids-standard/bids-specification/refs/heads/master/src/images/favicon.png)](https://bids-specification.readthedocs.io/en/stable/common-principles.html#imaging-files) | A community-developed standard for organizing and describing neuroscientific data. | [merged](https://github.com/bids-standard/bids-specification/pull/2392) | ## Gallery-like displays From cebca74e74246fcce8fb53584149e0894a832a4e Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Wed, 9 Sep 2026 05:41:17 -0500 Subject: [PATCH 3/4] Update ecosystem page --- resources/ecosystem/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/ecosystem/index.md b/resources/ecosystem/index.md index 7497cbf7d..66da1c59f 100644 --- a/resources/ecosystem/index.md +++ b/resources/ecosystem/index.md @@ -12,7 +12,7 @@ It fits microscope acquisition software, analysis pipelines, standards and exten | Name | Link | Description | Status | | -------- | ------- | ------- | ------ | | SpatialData | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/scverse/spatialdata) | An open and universal framework for processing spatial omics data. | [published](https://www.nature.com/articles/s41592-024-02212-x) | -| BIDS | [![image](https://raw.githubusercontent.com/bids-standard/bids-specification/refs/heads/master/src/images/favicon.png)](https://bids-specification.readthedocs.io/en/stable/common-principles.html#imaging-files) | A community-developed standard for organizing and describing neuroscientific data. | [merged](https://github.com/bids-standard/bids-specification/pull/2392) | +| BIDS | [![image](https://raw.githubusercontent.com/bids-standard/bids-specification/refs/heads/master/src/images/favicon.png)](https://bids-specification.readthedocs.io/en/stable/common-principles.html#imaging-files) | A community-developed standard for organizing and describing neuroscientific data, which supports OME-Zarr as a storage format for large imaging data. | [merged](https://github.com/bids-standard/bids-specification/pull/2392) | ## Gallery-like displays From b353503dfc47ec2d729a0192f623338812080f17 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Wed, 9 Sep 2026 05:43:36 -0500 Subject: [PATCH 4/4] Update glossary --- help-desk/index.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/help-desk/index.md b/help-desk/index.md index 90b0a3331..6c467f4d4 100644 --- a/help-desk/index.md +++ b/help-desk/index.md @@ -166,6 +166,8 @@ Jump to: ### B +**BIDS** - Brain Imaging Data Structure (BIDS) is a community-developed standard for organizing and describing neuroscientific data. The [BIDS specification supports OME-Zarr](https://bids-specification.readthedocs.io/en/stable/common-principles.html#imaging-files) as a storage format for large imaging data. + [Back to top](#glossary) ### C