InsightSoftwareConsortium
ome zarr notebook
Add OME-Zarr image registration notebook
A simple example that registers one timepoint in an IDR dataset to another.
We use the IDR dataset as it is a familiar reference sample OME-Zarr dataset in the community. This also demonstrates fetching the data dynamically from the cloud.
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Very interesting, Matt! I'm still trying to get it to work here locally but I got an error, on import ngff_zarr as nz, below here. Do you have a clue what I might have done wrong?
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
Cell In[4], line 4
2 import itk
3 from itkwidgets import view
----> 4 import ngff_zarr as nz
File ~\.conda\envs\ITKElxPoints\Lib\site-packages\ngff_zarr\__init__.py:6
1 # SPDX-FileCopyrightText: 2022-present Matt McCormick <[email protected]>
2 #
3 # SPDX-License-Identifier: MIT
5 from .__about__ import __version__
----> 6 from .cli_input_to_ngff_image import cli_input_to_ngff_image
7 from .config import config
8 from .detect_cli_io_backend import ConversionBackend, detect_cli_io_backend
File ~\.conda\envs\ITKElxPoints\Lib\site-packages\ngff_zarr\cli_input_to_ngff_image.py:3
1 import sys
----> 3 import zarr
4 from dask.array.image import imread as daimread
5 from rich import print
File ~\.conda\envs\ITKElxPoints\Lib\site-packages\zarr\__init__.py:2
1 from zarr._version import version as __version__
----> 2 from zarr.api.synchronous import (
3 array,
4 consolidate_metadata,
5 copy,
6 copy_all,
7 copy_store,
8 create,
9 create_array,
10 create_group,
11 empty,
12 empty_like,
13 full,
14 full_like,
15 group,
16 load,
17 ones,
18 ones_like,
19 open,
20 open_array,
21 open_consolidated,
22 open_group,
23 open_like,
24 save,
25 save_array,
26 save_group,
27 tree,
28 zeros,
29 zeros_like,
30 )
31 from zarr.core.array import Array, AsyncArray
32 from zarr.core.config import config
File ~\.conda\envs\ITKElxPoints\Lib\site-packages\zarr\api\synchronous.py:7
3 from typing import TYPE_CHECKING, Any, Literal
5 from typing_extensions import deprecated
----> 7 import zarr.api.asynchronous as async_api
8 import zarr.core.array
9 from zarr._compat import _deprecate_positional_args
File ~\.conda\envs\ITKElxPoints\Lib\site-packages\zarr\api\asynchronous.py:12
9 import numpy.typing as npt
10 from typing_extensions import deprecated
---> 12 from zarr.core.array import Array, AsyncArray, create_array, get_array_metadata
13 from zarr.core.array_spec import ArrayConfig, ArrayConfigLike
14 from zarr.core.buffer import NDArrayLike
File ~\.conda\envs\ITKElxPoints\Lib\site-packages\zarr\core\__init__.py:9
6 from __future__ import annotations
8 from zarr.core.buffer import Buffer, NDBuffer # noqa: F401
----> 9 from zarr.core.codec_pipeline import BatchedCodecPipeline
File ~\.conda\envs\ITKElxPoints\Lib\site-packages\zarr\core\codec_pipeline.py:20
18 from zarr.core.config import config
19 from zarr.core.indexing import SelectorTuple, is_scalar, is_total_slice
---> 20 from zarr.core.metadata.v2 import _default_fill_value
21 from zarr.registry import register_pipeline
23 if TYPE_CHECKING:
File ~\.conda\envs\ITKElxPoints\Lib\site-packages\zarr\core\metadata\__init__.py:3
1 from typing import TypeAlias, TypeVar
----> 3 from .v2 import ArrayV2Metadata, ArrayV2MetadataDict
4 from .v3 import ArrayV3Metadata, ArrayV3MetadataDict
6 ArrayMetadata: TypeAlias = ArrayV2Metadata | ArrayV3Metadata
File ~\.conda\envs\ITKElxPoints\Lib\site-packages\zarr\core\metadata\v2.py:9
6 from functools import cached_property
7 from typing import TYPE_CHECKING, TypedDict, cast
----> 9 import numcodecs.abc
11 from zarr.abc.metadata import Metadata
13 if TYPE_CHECKING:
File ~\.conda\envs\ITKElxPoints\Lib\site-packages\numcodecs\__init__.py:116
112 from numcodecs.json import JSON
114 register_codec(JSON)
--> 116 from numcodecs import vlen as vlen
117 from numcodecs.vlen import VLenArray, VLenBytes, VLenUTF8
119 register_codec(VLenUTF8)
File numcodecs\\vlen.pyx:1, in init numcodecs.vlen()
ImportError: numpy.core.multiarray failed to import (auto-generated because you didn't call 'numpy.import_array()' after cimporting numpy; use '<void>numpy._import_array' to disable if you are certain you don't need it).
@N-Dekker thanks for testing!
What versions of ngff_zarr, numpy, numcodecs, zarr do you have?
What versions of
ngff_zarr,numpy,numcodecs,zarrdo you have?
I just did a brand new install on a new pc. Now it says:
ImportError Traceback (most recent call last)
Cell In[1], line 5
3 import ngff_zarr as nz
4 from rich import print
----> 5 from zarr.storage import FSStore, LRUStoreCache
6 import zarr
7 import copy
ImportError: cannot import name 'FSStore' from 'zarr.storage' (C:\Users\...\.conda\envs\ITKElx\Lib\site-packages\zarr\storage\__init__.py)
I also printed the versions, as follows:
import sys
print(sys.version)
print("itk", itk.__version__)
import itkwidgets
print("itkwidgets", itkwidgets.__version__)
print("ngff_zarr", nz.__version__)
import numpy as np
print("numpy", np.__version__)
import numcodecs
print("numcodecs", numcodecs.__version__)
import zarr
print("zarr", zarr.__version__)
Which says:
3.11.11 | packaged by Anaconda, Inc. | (main, Dec 11 2024, 16:34:19) [MSC v.1929 64 bit (AMD64)]
itk 5.4.0
itkwidgets 0.32.6
ngff_zarr 0.12.1
numpy 2.2.2
numcodecs 0.15.0
zarr 3.0.1
Having pip-installed the "WindowsWheel311.zip" from the ITKElastix CI, from the last commit at the main, at https://github.com/InsightSoftwareConsortium/ITKElastix/actions/runs/12258642912
Do you have a clue?
@N-Dekker thanks for the information!
The issue is zarr 3, which was recently released. I'll have to make updates, but for now you could try with zarr 2.
Thanks Matt. I created a new environment, using zarr version 2:
3.11.11 | packaged by Anaconda, Inc. | (main, Dec 11 2024, 16:34:19) [MSC v.1929 64 bit (AMD64)]
itk 5.4.0
itkwidgets 0.32.6
ngff_zarr 0.12.1
numpy 1.26.4
numcodecs 0.14.1
zarr 2.13.3
Successfully moved one cell further, but unfortunately, now it says:
---------------------------------------------------------------------------
GroupNotFoundError Traceback (most recent call last)
Cell In[2], line 7
5 # Least recently used cache -- avoid re-fetching timepoints
6 lru_store = LRUStoreCache(fs_store, max_size=1e9)
----> 7 ome_zarr = nz.from_ngff_zarr(lru_store, version='0.3')
9 # 3D time series
10 print(ome_zarr)
File ~\.conda\envs\ITKElx-zarr2\Lib\site-packages\ngff_zarr\from_ngff_zarr.py:65, in from_ngff_zarr(store, validate, version)
59 if version and zarr_version_major >= 3:
60 format_kwargs = (
61 {"zarr_format": 2}
62 if packaging.version.parse(version) < packaging.version.parse("0.5")
63 else {"zarr_format": 3}
64 )
---> 65 root = zarr.open_group(store, mode="r", **format_kwargs)
66 root_attrs = root.attrs.asdict()
68 if not version:
File ~\.conda\envs\ITKElx-zarr2\Lib\site-packages\zarr\hierarchy.py:1374, in open_group(store, mode, cache_attrs, synchronizer, path, chunk_store, storage_options, zarr_version, meta_array)
1372 if contains_array(store, path=path):
1373 raise ContainsArrayError(path)
-> 1374 raise GroupNotFoundError(path)
1376 elif mode == 'w':
1377 init_group(store, overwrite=True, path=path, chunk_store=chunk_store)
GroupNotFoundError: group not found at path ''
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N-Dekker commented on 2025-01-27T13:43:42Z ----------------------------------------------------------------
Line #7. ome_zarr = nz.from_ngff_zarr(lru_store, version='0.3')
from_ngff_zarr returns a Multiscales object, so I would rather name the variable "multiscales" (instead of "ome_zar"). Just like in https://ngff-zarr.readthedocs.io/en/latest/python.html#read-an-ome-zarr
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N-Dekker commented on 2025-01-27T13:43:42Z ----------------------------------------------------------------
Line #5. vmin = ome_zarr.metadata.omero.channels[0].window.start
For my understanding, is the index [0] in channels[0] related to the index [0] in images[0]?
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N-Dekker commented on 2025-01-27T13:43:43Z ----------------------------------------------------------------
Line #2. view(fixed_image, vmin=vmin, vmax=vmax)
"vmin=vmin" and "vmax=vmax" look non-informative tautologies to me. I would like it better if it would say:
view(fixed_image, vmin=window.start, vmax=window.end)
Assuming window = multiscales.metadata.omero.channels[0].window
My review-notebook-app comments are only minor, stylish. No show-stopper.
I just wish I could make it run here locally!