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[ENH] Add OME-Zarr as a supported format for imaging data #2392

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[ENH] Add OME-Zarr as a supported format for imaging data #2392

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b03d776
Update common principles
kabilar Apr 12, 2026
ac3ecb2
Update schema
kabilar Apr 13, 2026
95edd49
Add OME-Zarr section
kabilar Apr 13, 2026
76f4397
Add trailing slash to ome-zarr extension to match microscopy extension
kabilar Apr 14, 2026
875ee53
Update common principles
kabilar Apr 12, 2026
62fcb64
Update schema
kabilar Apr 13, 2026
6f61c8a
Add OME-Zarr section
kabilar Apr 13, 2026
2fe2e8e
Add trailing slash to ome-zarr extension to match microscopy extension
kabilar Apr 14, 2026
d19dac2
Apply suggestion from @kabilar
kabilar Apr 21, 2026
c26e721
Merge branch 'omezarr' of https://github.com/kabilar/bids-specificati…
kabilar Apr 21, 2026
c3cd3f4
Merge branch 'master' of https://github.com/bids-standard/bids-specif…
kabilar Apr 21, 2026
383df17
Change `ZARR` to `Zarr`
kabilar Apr 21, 2026
e76e757
Add a link to the common principles
kabilar Apr 21, 2026
827e536
Add bids-examples dataset
kabilar Apr 22, 2026
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27 changes: 25 additions & 2 deletions src/common-principles.md
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Expand Up @@ -480,8 +480,13 @@ It is also RECOMMENDED to set the `SourceDatasets` field in `dataset_description

### Imaging files

All imaging data MUST be stored using the NIfTI file format. We RECOMMEND using
compressed NIfTI files (.nii.gz), either version 1.0 or 2.0. If using compressed files,
Imaging data SHOULD be stored using the NIfTI file format.
Large imaging data MAY instead be stored using the
[OME-Zarr (OME-NGFF)](https://ngff.openmicroscopy.org/) file format.
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@yarikoptic yarikoptic Apr 16, 2026

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I wonder if some schema-level check /could/should be added here based on some characteristics of the volume(s) -- e.g. any dimension having over 1k elements?

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@effigies effigies Apr 16, 2026

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Could: yes

checkname:
  issue: ...
  selectors:
    - type(nifti_header) != 'null'
  checks:
    - max(nifti_header.shape) <= 1000

Should: 🤷🏻

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@kabilar kabilar Apr 21, 2026

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Thanks. I don't feel too strongly here, but if we do add a check let's use level: warning.


#### NIfTI

We RECOMMEND using compressed NIfTI files (.nii.gz), either version 1.0 or 2.0. If using compressed files,
the gzip header SHOULD lack source filenames and timestamps. Imaging data SHOULD
be converted to the NIfTI format using a tool that provides as much of the NIfTI
header information (such as orientation and slice timing information) as
Expand All @@ -501,6 +506,24 @@ The [BIDS-validator](https://github.com/bids-standard/bids-validator)
will check for conflicts between the JSON file and the data recorded in the
NIfTI header.

#### OME-Zarr

[Zarr](https://zarr-specs.readthedocs.io/) is a chunked, cloud-optimized format that provides efficient access to
large multidimensional datasets without requiring a full download.
[OME-Zarr](https://ngff.openmicroscopy.org/), developed by the Open Microscopy Environment (OME),
extends Zarr with bioimaging-specific metadata.
OME-Zarr is particularly suitable for very large imaging volumes (for example, high-resolution
ex vivo MRI) where NIfTI would be impractical for streaming or web-based visualization.

OME-Zarr filesets are stored with the `.ome.zarr` extension.
Spatial metadata (such as the axis names and units, and coordinate transformations) SHOULD
be stored within the OME-Zarr metadata following the
[OME-Zarr version 0.5 specification](https://ngff.openmicroscopy.org/specifications/0.5/index.html)
(the latest released version).
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@yarikoptic yarikoptic Apr 16, 2026

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I thought to scream "duplication is evil!" but apparently we do not really disclose much in microscopy section about OME or NGFF

❯ git grep -i -e OME.Zarr -e ngff -- src/modality-specific-files/microscopy.md
src/modality-specific-files/microscopy.md:file's header. Further, OME-ZARR (sometimes referred to as OME-NGFF or NGFF) has been developed to provide improved
src/modality-specific-files/microscopy.md:-   [OME-ZARR/NGFF](https://ngff.openmicroscopy.org/latest/) (`.ome.zarr` directories)

but then we should at least take an opportunity to point to this section here from within that microscopy.md section. attn @bids-standard/bep031

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@kabilar kabilar Apr 21, 2026

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Good idea. I have just pushed a commit.

An example dataset containing an OME-Zarr can be found in the
[BIDS examples repository](https://github.com/bids-standard/bids-examples/tree/master/micr_XPCTzarr)
and can be used as helpful guidance when curating new datasets.

### Tabular files

Tabular data MUST be saved as plain-text, tab-delimited values (TSV) files
Expand Down
5 changes: 3 additions & 2 deletions src/modality-specific-files/microscopy.md
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Expand Up @@ -39,8 +39,9 @@ by the [Open Microscopy Environment](https://www.openmicroscopy.org/) for whole-
the [OME-TIFF file specifications](https://docs.openmicroscopy.org/ome-model/6.1.2/ome-tiff/file-structure.html).
The OME-TIFF file allows for multi-page TIFF files to store multiple image planes and supports
multi-resolution pyramidal tiled images. An OME-XML data block is also embedded inside the
file's header. Further, OME-ZARR (sometimes referred to as OME-NGFF or NGFF) has been developed to provide improved
file's header. Further, OME-Zarr (sometimes referred to as OME-NGFF or NGFF) has been developed to provide improved
access and storage for large data via chunked and compressed N-dimensional arrays.
For details on using OME-Zarr in BIDS, see the [Common Principles](../common-principles.md#ome-zarr).

The BIDS standard accepts microscopy data in a number of file formats to accommodate datasets
stored in 2D image formats and whole-slide imaging formats, to accommodate lossless and lossy
Expand All @@ -57,7 +58,7 @@ Microscopy raw data MUST be stored in one of the following formats:
(`.ome.tif` for standard TIFF files or `.ome.btf` for
[BigTIFF](https://web.archive.org/web/20240706160214/https://www.awaresystems.be/imaging/tiff/bigtiff.html) files)

- [OME-ZARR/NGFF](https://ngff.openmicroscopy.org/latest/) (`.ome.zarr` directories)
- [OME-Zarr/NGFF](https://ngff.openmicroscopy.org/latest/) (`.ome.zarr` directories)

### Modality suffixes
Microscopy data currently support the following imaging modalities:
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1 change: 1 addition & 0 deletions src/schema/meta/templates.yaml
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Expand Up @@ -88,6 +88,7 @@ deriv:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
entities:
$ref: meta.templates.deriv.spatial.entities
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10 changes: 10 additions & 0 deletions src/schema/rules/files/raw/anat.yaml
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Expand Up @@ -16,6 +16,7 @@ nonparametric:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- anat
Expand Down Expand Up @@ -46,6 +47,7 @@ parametric:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- anat
Expand All @@ -59,6 +61,7 @@ defacemask:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- anat
Expand All @@ -73,6 +76,7 @@ megre:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- anat
Expand All @@ -88,6 +92,7 @@ mese:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- anat
Expand All @@ -104,6 +109,7 @@ multiflip:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- anat
Expand All @@ -120,6 +126,7 @@ multiinversion:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- anat
Expand All @@ -135,6 +142,7 @@ mp2rage:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- anat
Expand All @@ -153,6 +161,7 @@ vfamt:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- anat
Expand All @@ -170,6 +179,7 @@ mtr:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- anat
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3 changes: 3 additions & 0 deletions src/schema/rules/files/raw/dwi.yaml
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Expand Up @@ -5,6 +5,7 @@ dwi:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
- .bvec
- .bval
Expand All @@ -22,6 +23,7 @@ sbref:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- dwi
Expand All @@ -41,6 +43,7 @@ ScannerDerivatives:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- dwi
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8 changes: 8 additions & 0 deletions src/schema/rules/files/raw/fmap.yaml
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Expand Up @@ -11,6 +11,7 @@ fieldmaps:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- fmap
Expand All @@ -25,6 +26,7 @@ pepolar:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
- .bval
- .bvec
Expand All @@ -38,6 +40,7 @@ pepolar_m0scan:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- fmap
Expand All @@ -48,6 +51,7 @@ TB1DAM:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- fmap
Expand All @@ -63,6 +67,7 @@ TB1EPI:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- fmap
Expand All @@ -82,6 +87,7 @@ RFFieldMaps:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- fmap
Expand All @@ -98,6 +104,7 @@ TB1SRGE:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- fmap
Expand All @@ -116,6 +123,7 @@ parametric:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- fmap
1 change: 1 addition & 0 deletions src/schema/rules/files/raw/func.yaml
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Expand Up @@ -7,6 +7,7 @@ func:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- func
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1 change: 1 addition & 0 deletions src/schema/rules/files/raw/perf.yaml
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Expand Up @@ -6,6 +6,7 @@ asl:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- perf
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1 change: 1 addition & 0 deletions src/schema/rules/files/raw/pet.yaml
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Expand Up @@ -5,6 +5,7 @@ pet:
extensions:
- .nii.gz
- .nii
- .ome.zarr/
- .json
datatypes:
- pet
Expand Down
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