yaozarrs 0.0.1rc2

Yet another ome-zarr model.

yaozarrs ‼️

Yet Another Ome-ZARR Schema!

Oh no, not another one 🤦

First, let me apologize. The last thing the world needs is yet another ome-zarr model. However, I was unable to find a minimal ome-zarr model that simply represents the spec, without introducing additional I/O features or dependencies. Please read the Existing Projects section for more context.

Installation

pip install yaozarrs

# or, to load/validate local/remote zarr stores:
pip install yaozarrs[io]

Usage

Here are some things you can do with yaozarrs.

1. Construct valid ome-zarr JSON documents for creating ome-zarr groups
2. Validate & load existing JSON documents
3. Validate arbitrary python objects as an OME-NGFF object
4. Validate any zarr store using the CLI
5. Validate any zarr store programmatically
6. Open zarr arrays using zarr-python or tensorstore

Construct valid ome-zarr JSON documents for creating ome-zarr groups

This is useful if you are creating OME-Zarr files directly. Since this package has no dependencies beyond pydantic, it allows downstream projects to use a common model, without enforcing a specific mechanism for data I/O (e.g. using zarr, tensorstore, acquire-zarr, etc),

from yaozarrs import v05
from pathlib import Path

scale = v05.Multiscale(
    name="scale0",
    axes=[v05.SpaceAxis(name="x", type="space"), v05.SpaceAxis(name="y", type="space")],
    datasets=[
        v05.Dataset(
            path="0",
            coordinateTransformations=[v05.ScaleTransformation(scale=[1, 1])],
        ),
        v05.Dataset(
            path="1",
            coordinateTransformations=[v05.ScaleTransformation(scale=[1, 1])],
        ),
    ],
)

img = v05.Image(multiscales=[scale])
zarr_json = v05.OMEZarrGroupJSON(attributes={"ome": img})
json_data = zarr_json.model_dump_json(exclude_unset=True)
Path("zarr.json").write_text(json_data)

Validate & load existing JSON documents

If you have an existing JSON document, you can validate and load it, and benefit from IDE autocompletion and type hints.

from pathlib import Path
import yaozarrs

json_string = Path("zarr.json").read_text()
obj = yaozarrs.validate_ome_json(json_string)

# OMEZarrGroupJSON(
#     zarr_format=3,
#     node_type='group',
#     attributes=OMEAttributes(
#         ome=Image(
#             version='0.5',
#             multiscales=[
#                 Multiscale(
#                     name='scale0',
#                     axes=[SpaceAxis(name='x', type='space', unit=None), SpaceAxis(name='y', type='space', unit=None)],
#                     datasets=[
#                         Dataset(path='0', coordinateTransformations=[ScaleTransformation(type='scale', scale=[0.0, 1.0])]),
#                         Dataset(path='1', coordinateTransformations=[ScaleTransformation(type='scale', scale=[0.0, 1.0])])
#                     ],
#                     coordinateTransformations=None,
#                     type=None,
#                     metadata=None
#                 )
#             ],
#             omero=None
#         )
#     )
# )

Validate arbitrary python objects as an OME-NGFF object

validate_ome_object and validate_ome_json accept a broad range of inputs, and will cast to an appropriate model if possible.

import yaozarrs

obj = yaozarrs.validate_ome_object(
  {'version': '0.5', 'series': ["0", "1"]}
)
print(obj)
# Series(version='0.5', series=['0', '1'])

Validate any zarr store using the CLI

[!IMPORTANT]
Requires fsspec. install with pip install yaozarrs[io]

The CLI command provides a quick way to validate any zarr store as an OME-Zarr store. Here, "store" here refers to any URI (local path, http(s) url, s3 url, etc) or a zarr-python zarr.Group.

$ yaozarrs validate https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.5/idr0062A/6001240_labels.zarr
✓ Valid OME-Zarr store
  Version: 0.5
  Type: Image

[!TIP]
Use uvx for quick validation of any URI, without pip installing the package.

uvx "yaozarrs[io]" validate https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.5/idr0062A/6001240_labels.zarr

Storage Validation Errors

Validation errors that relate to the structure of the OME-Zarr itself (as opposed to metadata) are collected and presented similarly to pydantic validation errors for the metadata:

location
  description [context]

An example validation error (for a file that has many problems):

uvx "yaozarrs[io]" validate https://raw.githubusercontent.com/tlambert03/yaozarrs/refs/heads/main/tests/data/broken/broken_v05.ome.zarr/

yaozarrs._storage.StorageValidationError: 14 validation error(s) for StorageValidationError
ome.plate.wells.0.well.images.0.multiscales.0.datasets.0.path
  Dataset path '0' not found in zarr group [type=dataset_path_not_found, fs_path='broken_v05.ome.zarr/A/1/0/0', expected='zarr array']

ome.plate.wells.0.well.images.0.labels.labels.0
  Label path 'annotations' not found in labels group [type=label_path_not_found, fs_path='broken_v05.ome.zarr/A/1/0/labels/annotations', expected='zarr group']

ome.plate.wells.0.well.images.1.labels.labels.0
  Label path 'annotations' is not a zarr group [type=label_path_not_group, fs_path='broken_v05.ome.zarr/A/1/1/labels/annotations', expected='group', found='array']

ome.plate.wells.1.path
  Well path 'A/2' is not a zarr group [type=well_path_not_group, fs_path='broken_v05.ome.zarr/A/2', expected='group', found='array']

ome.plate.wells.2.well.images.0.labels.labels.0
  Label path 'annotations' does not contain valid Image ('multiscales') metadata [type=label_image_invalid, path='annotations']
  1 validation error for tagged-union[LabelImage,Image,Plate,Bf2Raw,Well,LabelsGroup,Series]
    Unable to extract tag using discriminator _discriminate_ome_v05_metadata() [type=union_tag_not_found, input_value={}, input_type=dict]
      For further information visit https://errors.pydantic.dev/2.12/v/union_tag_not_found

ome.plate.wells.3.well.images.0.multiscales.0.datasets.0.path
  Dataset '0' has 5 dimensions but axes specify 3 [type=dataset_dimension_mismatch, fs_path='broken_v05.ome.zarr/B/1/0/0', actual_ndim=5, expected_ndim=3, axes=['c', 'y', 'x']]

ome.plate.wells.3.well.images.0.labels.labels.0.multiscales.0.datasets.0.path
  Label array '0' has non-integer dtype 'float32'. Labels must use integer types. [type=label_non_integer_dtype, path='0', dtype='float32']

ome.plate.wells.4.well.images.0.multiscales.0.datasets.0.path
  Dataset path '0' exists but is not a zarr array [type=dataset_not_array, fs_path='broken_v05.ome.zarr/B/2/0/0', expected='array', found='group']

ome.plate.wells.4.well.images.1.multiscales.0.datasets.0.path.dimension_names
  Array dimension_names ['wrong', 'names', 'here'] don't match axes names ['c', 'y', 'x'] [type=dimension_names_mismatch, expected=['c', 'y', 'x'], actual=['wrong', 'names', 'here']]

ome.plate.wells.5.well.images.0.labels
  Found 'labels' path but it is a <class 'yaozarrs._zarr.ZarrArray'>, not a zarr group [type=labels_not_group, expected='group', found='ZarrArray']

ome.plate.wells.5.well.images.1.path
  Field path '1' is not a zarr group [type=field_path_not_group, fs_path='broken_v05.ome.zarr/B/3/1', expected='group', found='array']

ome.plate.wells.6.well.images.1.path
  Field path '1' not found in well group [type=field_path_not_found, fs_path='broken_v05.ome.zarr/C/1/1', expected='zarr group']

ome.plate.wells.7.well.images.0
  Field path '0' does not contain valid Image metadata [type=field_image_invalid, fs_path='broken_v05.ome.zarr/C/2/0']
  1 validation error for tagged-union[LabelImage,Image,Plate,Bf2Raw,Well,LabelsGroup,Series]
  image.multiscales
    Value should have at least 1 item after validation, not 0 [type=too_short, input_value=[], input_type=list]
      For further information visit https://errors.pydantic.dev/2.12/v/too_short

ome.plate.wells.8
  Well path 'C/3' does not contain valid Well metadata [type=well_invalid, path='C/3']
  1 validation error for tagged-union[LabelImage,Image,Plate,Bf2Raw,Well,LabelsGroup,Series]
    Unable to extract tag using discriminator _discriminate_ome_v05_metadata() [type=union_tag_not_found, input_value={}, input_type=dict]
      For further information visit https://errors.pydantic.dev/2.12/v/union_tag_not_found

Validate any zarr store programmatically

[!IMPORTANT]
Requires fsspec. install with pip install yaozarrs[io]

import yaozarrs

yaozarrs.validate_zarr_store("https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.5/idr0062A/6001240_labels.zarr")

Open zarr arrays using zarr-python or tensorstore

[!IMPORTANT]

• to_tensorstore() requires tensorstore
• to_zarr_python() requires zarr

This package does not depend on zarr or tensorstore, even for validating OME-Zarr stores. (It uses a minimal representation of a zarr group internally, backed by fsspec.) If you would like to actually open arrays, you can use either zarr or tensorstore directly.

from yaozarrs import open_group

group = open_group("https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.5/idr0062A/6001240_labels.zarr")
array = group['0']
# <ZarrArray https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.5/idr0062A/6001240_labels.zarr/0>

# read bytes using tensorstore or zarr-python:
ts_array = array.to_tensorstore() # isinstance(ts_array, tensorstore.TensorStore)
zarr_array = array.to_zarr_python() # isinstance(zarr_array, zarr.Array)

# inspect the OME metadata associated with the group:
print(group.ome_metadata())
# Image(
#     version='0.5',
#     multiscales=[
#         Multiscale(
#             name=None,
#             axes=[
#                 ChannelAxis(name='c', type='channel', unit=None),
#                 SpaceAxis(
#                     name='z',
#                     type='space',
#                     unit='micrometer'
#                 ),
#                 SpaceAxis(
#                     name='y',
#                     type='space',
#                     unit='micrometer'
#                 ),
#                 SpaceAxis(
#                     name='x',
#                     type='space',
#                     unit='micrometer'
#                 )
#             ],
#             datasets=[
#                 Dataset(
#                     path='0',
#                     coordinateTransformations=[
#                         ScaleTransformation(
#                             type='scale',
#                             scale=[
#                                 1.0,
#                                 0.5002025531914894,
#                                 0.3603981534640209,
#                                 0.3603981534640209
#                             ]
#                         )
#                     ]
#                 ),
#                 Dataset(
#                     path='1',
#                     coordinateTransformations=[
#                         ScaleTransformation(
#                             type='scale',
#                             scale=[
#                                 1.0,
#                                 0.5002025531914894,
#                                 0.7207963069280418,
#                                 0.7207963069280418
#                             ]
#                         )
#                     ]
#                 ),
#                 Dataset(
#                     path='2',
#                     coordinateTransformations=[
#                         ScaleTransformation(
#                             type='scale',
#                             scale=[
#                                 1.0,
#                                 0.5002025531914894,
#                                 1.4415926138560835,
#                                 1.4415926138560835
#                             ]
#                         )
#                     ]
#                 )
#             ],
#             coordinateTransformations=None,
#             type=None,
#             metadata=None
#         )
#     ],
#     omero=Omero(
#         channels=[
#             OmeroChannel(
#                 window=OmeroWindow(
#                     start=0.0,
#                     min=0.0,
#                     end=1500.0,
#                     max=65535.0
#                 ),
#                 label='LaminB1',
#                 family='linear',
#                 color='0000FF',
#                 active=True,
#                 inverted=False,
#                 coefficient=1.0
#             ),
#             OmeroChannel(
#                 window=OmeroWindow(
#                     start=0.0,
#                     min=0.0,
#                     end=1500.0,
#                     max=65535.0
#                 ),
#                 label='Dapi',
#                 family='linear',
#                 color='FFFF00',
#                 active=True,
#                 inverted=False,
#                 coefficient=1.0
#             )
#         ],
#         id=1
#     )
# )

Existing Projects

You should first check these existing packages to see if they meet your needs:

• ome-zarr-models-py.
  This project has garnered strong community attention and aligns well with many use cases.
  For my particular goals, I found a few things diverged from what I need.

  1. It offers convenient I/O helpers (based on and requiring zarr-python) that are great in many contexts, but I wanted to explore a version with no I/O assumptions – just classes mirroring the schema – without the zarr dep.

     There are issues & PRs to this effect:

     • https://github.com/ome-zarr-models/ome-zarr-models-py/issues/161
     • https://github.com/ome-zarr-models/ome-zarr-models-py/pull/280

     but since ome-zarr-models-py also depends on pydantic-zarr, that library will also need to be modified to remove the zarr dependency.

     • https://github.com/zarr-developers/pydantic-zarr/pull/112

  2. It currently pins to Python 3.11+ (presumably following NEP-29/SPEC-0), whereas I prefer to match the official python EOL schedule (supporting 3.10 until mid 2026).

  3. Its inheritance and generics provide powerful abstractions, though for my experiments I wanted something simpler that just mirrors the spec.

  Ideally, this kind of minimal approach could help inform future directions for ome-zarr-models-py, and I’d be glad to see ideas converge over time.

• pydantic-ome-ngff. Deprecated.

• ngff-zarr. This also contains models, but brings along far more dependencies and assumptions (and functionality) than ome-zarr-models-py.

• ome-zarr. This is a general toolkit, that provides functions for reading and writing OME-ZARR, among other things, but brings in many dependencies (zarr, scikit-image, dask,...) and doesn't export metadata models.

In the meantime:

This is an experimental package, where I can develop minimal models for my applications. The hope would be some future unification, provided the community can agree on a common denominator of features.

Ultimately, I want a schema-first, I/O-second library.