From a56bb581402696d54a5604234392cdaebc56d18b Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Wed, 9 Sep 2026 06:04:48 -0500 Subject: [PATCH 1/4] doc: Add NIfTI-Zarr format and converter --- resources/ecosystem/index.md | 1 + resources/tools/index.md | 1 + 2 files changed, 2 insertions(+) diff --git a/resources/ecosystem/index.md b/resources/ecosystem/index.md index 10c92ea10..adb2d81b9 100644 --- a/resources/ecosystem/index.md +++ b/resources/ecosystem/index.md @@ -13,6 +13,7 @@ It fits microscope acquisition software, analysis pipelines, standards and exten | -------- | ------- | ------- | ------ | | 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) | +| NIfTI-Zarr | [![image](https://avatars.githubusercontent.com/u/155756215)](https://github.com/neuroscales/nifti-zarr) | An OME-Zarr format for neuroimaging data that embeds a NIfTI header alongside the OME-Zarr metadata, with a Python implementation in [nifti-zarr-py](https://github.com/neuroscales/nifti-zarr-py). | [release candidate](https://github.com/neuroscales/nifti-zarr) | ## Gallery-like displays diff --git a/resources/tools/index.md b/resources/tools/index.md index 89642e6e5..1de94093d 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -79,6 +79,7 @@ Check out the [readers and writers below](#zarr-readers--writers) to interact wi | multiscale-spatial-image | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/spatial-image/multiscale-spatial-image) | Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-Zarr. | Reading & Writing | | nd2 | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/tlambert03/nd2) | A Python library for reading nd2 files with native export to OME-Zarr, supporting multi-well plates and complete metadata preservation. | | Nextflow (nf-omezarr) | [Nextflow logo](https://github.com/JaneliaSciComp/nf-omezarr) | A Nextflow pipeline for converting directories of images to OME-Zarr using bioformats2raw | +| nifti-zarr-py | [![image](https://avatars.githubusercontent.com/u/155756215)](https://github.com/neuroscales/nifti-zarr-py) | A Python implementation of the [nifti-zarr](https://github.com/neuroscales/nifti-zarr) specification, converting between NIfTI and NIfTI-Zarr (an OME-Zarr format carrying NIfTI metadata) and reading NIfTI-Zarr directly. | | PyMIF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/grinic/pymif) | A modular Python package to read, visualize, and convert multiscale microscopy image data from various microscope platforms to OME-Zarr. | | stack-to-chunk | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://stack-to-chunk.readthedocs.io) | A Python library to convert stacks of 2D images to OME-Zarr with minimal memory use and maximum concurrency. | | stack_to_multiscale_ngff | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/CBI-PITT/stack_to_multiscale_ngff) | A tool for converting multi-terabyte stacks of images into a multiscale OME-Zarr. | From 9b17565d5b622747f92d8448c59fcdaca4386c71 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Wed, 9 Sep 2026 06:14:29 -0500 Subject: [PATCH 2/4] Reduce logo size --- resources/ecosystem/index.md | 2 +- resources/tools/index.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/resources/ecosystem/index.md b/resources/ecosystem/index.md index adb2d81b9..da918c90b 100644 --- a/resources/ecosystem/index.md +++ b/resources/ecosystem/index.md @@ -13,7 +13,7 @@ It fits microscope acquisition software, analysis pipelines, standards and exten | -------- | ------- | ------- | ------ | | 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) | -| NIfTI-Zarr | [![image](https://avatars.githubusercontent.com/u/155756215)](https://github.com/neuroscales/nifti-zarr) | An OME-Zarr format for neuroimaging data that embeds a NIfTI header alongside the OME-Zarr metadata, with a Python implementation in [nifti-zarr-py](https://github.com/neuroscales/nifti-zarr-py). | [release candidate](https://github.com/neuroscales/nifti-zarr) | +| NIfTI-Zarr | [![image](https://avatars.githubusercontent.com/u/155756215?s=60)](https://github.com/neuroscales/nifti-zarr) | An OME-Zarr format for neuroimaging data that embeds a NIfTI header alongside the OME-Zarr metadata, with a Python implementation in [nifti-zarr-py](https://github.com/neuroscales/nifti-zarr-py). | [release candidate](https://github.com/neuroscales/nifti-zarr) | ## Gallery-like displays diff --git a/resources/tools/index.md b/resources/tools/index.md index 1de94093d..4bae03195 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -79,7 +79,7 @@ Check out the [readers and writers below](#zarr-readers--writers) to interact wi | multiscale-spatial-image | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/spatial-image/multiscale-spatial-image) | Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-Zarr. | Reading & Writing | | nd2 | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/tlambert03/nd2) | A Python library for reading nd2 files with native export to OME-Zarr, supporting multi-well plates and complete metadata preservation. | | Nextflow (nf-omezarr) | [Nextflow logo](https://github.com/JaneliaSciComp/nf-omezarr) | A Nextflow pipeline for converting directories of images to OME-Zarr using bioformats2raw | -| nifti-zarr-py | [![image](https://avatars.githubusercontent.com/u/155756215)](https://github.com/neuroscales/nifti-zarr-py) | A Python implementation of the [nifti-zarr](https://github.com/neuroscales/nifti-zarr) specification, converting between NIfTI and NIfTI-Zarr (an OME-Zarr format carrying NIfTI metadata) and reading NIfTI-Zarr directly. | +| nifti-zarr-py | [![image](https://avatars.githubusercontent.com/u/155756215?s=60)](https://github.com/neuroscales/nifti-zarr-py) | A Python implementation of the [nifti-zarr](https://github.com/neuroscales/nifti-zarr) specification, converting between NIfTI and NIfTI-Zarr (an OME-Zarr format carrying NIfTI metadata) and reading NIfTI-Zarr directly. | | PyMIF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/grinic/pymif) | A modular Python package to read, visualize, and convert multiscale microscopy image data from various microscope platforms to OME-Zarr. | | stack-to-chunk | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://stack-to-chunk.readthedocs.io) | A Python library to convert stacks of 2D images to OME-Zarr with minimal memory use and maximum concurrency. | | stack_to_multiscale_ngff | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/CBI-PITT/stack_to_multiscale_ngff) | A tool for converting multi-terabyte stacks of images into a multiscale OME-Zarr. | From 140b56faed29cb6cae162446650ad11b37505d4f Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Wed, 9 Sep 2026 06:34:19 -0500 Subject: [PATCH 3/4] Update logo dimensions --- resources/ecosystem/index.md | 2 +- resources/tools/index.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/resources/ecosystem/index.md b/resources/ecosystem/index.md index da918c90b..4c39d89b7 100644 --- a/resources/ecosystem/index.md +++ b/resources/ecosystem/index.md @@ -13,7 +13,7 @@ It fits microscope acquisition software, analysis pipelines, standards and exten | -------- | ------- | ------- | ------ | | 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) | -| NIfTI-Zarr | [![image](https://avatars.githubusercontent.com/u/155756215?s=60)](https://github.com/neuroscales/nifti-zarr) | An OME-Zarr format for neuroimaging data that embeds a NIfTI header alongside the OME-Zarr metadata, with a Python implementation in [nifti-zarr-py](https://github.com/neuroscales/nifti-zarr-py). | [release candidate](https://github.com/neuroscales/nifti-zarr) | +| NIfTI-Zarr | NIfTI-Zarr logo | An OME-Zarr format for neuroimaging data that embeds a NIfTI header alongside the OME-Zarr metadata, with a Python implementation in [nifti-zarr-py](https://github.com/neuroscales/nifti-zarr-py). | [release candidate](https://github.com/neuroscales/nifti-zarr) | ## Gallery-like displays diff --git a/resources/tools/index.md b/resources/tools/index.md index 4bae03195..1eb77fac8 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -79,7 +79,7 @@ Check out the [readers and writers below](#zarr-readers--writers) to interact wi | multiscale-spatial-image | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/spatial-image/multiscale-spatial-image) | Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-Zarr. | Reading & Writing | | nd2 | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/tlambert03/nd2) | A Python library for reading nd2 files with native export to OME-Zarr, supporting multi-well plates and complete metadata preservation. | | Nextflow (nf-omezarr) | [Nextflow logo](https://github.com/JaneliaSciComp/nf-omezarr) | A Nextflow pipeline for converting directories of images to OME-Zarr using bioformats2raw | -| nifti-zarr-py | [![image](https://avatars.githubusercontent.com/u/155756215?s=60)](https://github.com/neuroscales/nifti-zarr-py) | A Python implementation of the [nifti-zarr](https://github.com/neuroscales/nifti-zarr) specification, converting between NIfTI and NIfTI-Zarr (an OME-Zarr format carrying NIfTI metadata) and reading NIfTI-Zarr directly. | +| nifti-zarr-py | NIfTI-Zarr logo | A Python implementation of the [nifti-zarr](https://github.com/neuroscales/nifti-zarr) specification, converting between NIfTI and NIfTI-Zarr (an OME-Zarr format carrying NIfTI metadata) and reading NIfTI-Zarr directly. | | PyMIF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/grinic/pymif) | A modular Python package to read, visualize, and convert multiscale microscopy image data from various microscope platforms to OME-Zarr. | | stack-to-chunk | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://stack-to-chunk.readthedocs.io) | A Python library to convert stacks of 2D images to OME-Zarr with minimal memory use and maximum concurrency. | | stack_to_multiscale_ngff | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/CBI-PITT/stack_to_multiscale_ngff) | A tool for converting multi-terabyte stacks of images into a multiscale OME-Zarr. | From 6429888f773b8746e219aea23a91d59776a1e030 Mon Sep 17 00:00:00 2001 From: Kabilar Gunalan Date: Wed, 9 Sep 2026 09:41:29 -0500 Subject: [PATCH 4/4] Update resources/tools/index.md Co-authored-by: Tiago Lubiana --- resources/tools/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 1eb77fac8..9691973e1 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -79,7 +79,7 @@ Check out the [readers and writers below](#zarr-readers--writers) to interact wi | multiscale-spatial-image | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/spatial-image/multiscale-spatial-image) | Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-Zarr. | Reading & Writing | | nd2 | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/tlambert03/nd2) | A Python library for reading nd2 files with native export to OME-Zarr, supporting multi-well plates and complete metadata preservation. | | Nextflow (nf-omezarr) | [Nextflow logo](https://github.com/JaneliaSciComp/nf-omezarr) | A Nextflow pipeline for converting directories of images to OME-Zarr using bioformats2raw | -| nifti-zarr-py | NIfTI-Zarr logo | A Python implementation of the [nifti-zarr](https://github.com/neuroscales/nifti-zarr) specification, converting between NIfTI and NIfTI-Zarr (an OME-Zarr format carrying NIfTI metadata) and reading NIfTI-Zarr directly. | +| nifti-zarr-py | NIfTI-Zarr logo | A Python implementation of the [nifti-zarr](https://github.com/neuroscales/nifti-zarr) specification, converting between NIfTI and NIfTI-Zarr (an OME-Zarr format carrying NIfTI metadata) and reading NIfTI-Zarr directly. | | PyMIF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/grinic/pymif) | A modular Python package to read, visualize, and convert multiscale microscopy image data from various microscope platforms to OME-Zarr. | | stack-to-chunk | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://stack-to-chunk.readthedocs.io) | A Python library to convert stacks of 2D images to OME-Zarr with minimal memory use and maximum concurrency. | | stack_to_multiscale_ngff | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/CBI-PITT/stack_to_multiscale_ngff) | A tool for converting multi-terabyte stacks of images into a multiscale OME-Zarr. |