bioio-ome-zarr 3.3.0

A BioIO reader plugin for reading Zarr files in the OME format.

bioio-ome-zarr

A BioIO reader plugin for reading OME ZARR images using ome-zarr

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Documentation

See the full documentation on our GitHub pages site - the generic use and installation instructions there will work for this package.

Information about the base reader this package relies on can be found in the bioio-base repository here

Installation

Stable Release: pip install bioio-ome-zarr
Development Head: pip install git+https://github.com/bioio-devs/bioio-ome-zarr.git

Example Usage (see full documentation for more examples)

Install bioio-ome-zarr alongside bioio:

pip install bioio bioio-ome-zarr

This example shows a simple use case for just accessing the pixel data of the image by explicitly passing this Reader into the BioImage. Passing the Reader into the BioImage instance is optional as bioio will automatically detect installed plug-ins and auto-select the most recently installed plug-in that supports the file passed in.

from bioio import BioImage
import bioio_ome_zarr

img = BioImage("my_file.zarr", reader=bioio_ome_zarr.Reader)
img.data

Reading from AWS S3

To read from private S3 buckets, credentials must be configured. Public buckets can be accessed without credentials.

from bioio import BioImage
path = "https://allencell.s3.amazonaws.com/aics/nuc-morph-dataset/hipsc_fov_nuclei_timelapse_dataset/hipsc_fov_nuclei_timelapse_data_used_for_analysis/baseline_colonies_fov_timelapse_dataset/20200323_09_small/raw.ome.zarr"
image = BioImage(path)
print(image.get_image_dask_data())

Writing OME-Zarr Stores

The OMEZarrWriter can write both Zarr v2 (NGFF 0.4) and Zarr v3 (NGFF 0.5) formats.

basic writer example (2D YX)

from bioio_ome_zarr.writers import OMEZarrWriter
import numpy as np

# Minimal 2D example (Y, X)
data = np.random.randint(0, 255, size=(64, 64), dtype=np.uint8)

writer = OMEZarrWriter(
    store="basic.zarr",
    level_shapes=(64, 64),   # (Y, X)
    dtype=data.dtype,
)

# Write the data to the store
writer.write_full_volume(data)

5D (TCZYX), with one extra resolution level

from bioio_ome_zarr.writers import OMEZarrWriter, Channel
import numpy as np

level_shapes = [
    (2, 3, 4, 256, 256),  # L0 full res
    (2, 3, 4, 128, 128),  # L1 downsampled Y/X by 2
]

data = np.random.randint(0, 255, size=level_shapes[0], dtype=np.uint8)
channels = [Channel(label=f"c{i}", color="FF0000") for i in range(data.shape[1])]

writer = OMEZarrWriter(
    store="output.zarr",
    level_shapes=level_shapes,
    dtype=data.dtype,
    zarr_format=3,  # 2 for Zarr v2
    channels=channels,
    axes_names=["t", "c", "z", "y", "x"],
    axes_types=["time", "channel", "space", "space", "space"],
    axes_units=[None, None, "micrometer", "micrometer", "micrometer"],
)

writer.write_full_volume(data)

Full writer parameters and API

Parameter	Type	Description
store	str or zarr.storage.StoreLike	Filesystem path, fsspec URL, or Store-like for the root group.
level_shapes	Sequence[int] or Sequence[Sequence[int]]	Either a single N‑D shape (one level) or an explicit per‑level list of shapes (level 0 first). Examples above.
dtype	np.dtype or str	On‑disk dtype (e.g., uint8, uint16).
chunk_shape	Sequence[int] or Sequence[Sequence[int]] or None	Chunk shape: single (applied to all levels) or per‑level. If None, a ≈16 MiB chunk is suggested per level via multiscale_chunk_size_from_memory_target.
shard_shape	Sequence[int] or Sequence[Sequence[int]] or None	Zarr v3 only. Single or per‑level shard shapes. Each shard dim must be an integer multiple of the corresponding chunk dim.
compressor	BloscCodec (v3) or numcodecs.abc.Codec (v2) or None	Compression codec. Defaults to zstd + bitshuffle.
zarr_format	Literal[2,3]	Target Zarr format – 2 (NGFF 0.4) or 3 (NGFF 0.5). Default 3.
image_name	str or None	Name used in multiscales metadata. Default: "Image".
channels	list[Channel] or None	OMERO‑style channel metadata.
rdefs	dict or None	OMERO rendering defaults.
creator_info	dict or None	Optional creator block (NGFF 0.5).
root_transform	dict[str, Any] or None	Optional transform placed at multiscale root.
axes_names	list[str] or None	Axis names; defaults to the last N of ["t","c","z","y","x"].
axes_types	list[str] or None	Axis types; defaults to ["time","channel","space", …].
axes_units	list[str]orNone	Physical units per axis.
physical_pixel_size	list[float] or None	Level‑0 physical scale per axis.

Methods

• write_full_volume(input_data: np.ndarray | dask.array.Array) -> None Write level‑0 and all declared pyramid levels. NumPy arrays are wrapped into Dask using level‑0 chunks.

• write_timepoints(data: np.ndarray | dask.array.Array, *, start_T_src=0, start_T_dest=0, total_T: int | None = None) -> None Stream along the T axis from data into the store. Spatial axes are downsampled for lower levels; T/C are preserved.

• preview_metadata() -> dict[str, Any] Returns the NGFF metadata dict(s) that would be written (no IO).

Writing a full volume (NumPy or Dask)

# NumPy (wrapped automatically)
writer.write_full_volume(data)

# Or pass an explicit Dask array
import dask.array as da
writer.write_full_volume(da.from_array(data, chunks=(1, 1, 1, 64, 64)))

Writing timepoints in batches (streaming along T)

# Suppose your writer axes include "T"; write timepoints in flexible batches
from bioio import BioImage
import dask.array as da

bioimg = BioImage("/path/to/any/bioimage")
data = bioimg.get_image_dask_data()

# Write the entire timeseries at once
writer.write_timepoints(data)

# Write in 5-timepoint batches
for t in range(0, data.shape[0], 5):
    writer.write_timepoints(
    data,
    start_T_src=t,
    start_T_dest=t,
    total_T=5,
    )

# Write source timepoints [10:20] into destination positions [50:60]
writer.write_timepoints(
    data,
    start_T_src=10,
    start_T_dest=50,
    total_T=10,
)

Custom chunking per level

# Provide one chunk shape per level; must match ndim
chunk_shape = (
    (1, 1, 1, 64, 64),  # level 0
    (1, 1, 1, 32, 32),  # level 1
)
writer = OMEZarrWriter(
    store="custom_chunks.zarr",
    level_shapes=[(1, 1, 2, 256, 256), (1, 1, 2, 128, 128)],
    dtype="uint16",
    zarr_format=3,
    chunk_shape=chunk_shape,
)

# Example data matching the declared shape
arr = np.random.randint(0, 65535, size=(1, 1, 2, 256, 256), dtype=np.uint16)
writer.write_full_volume(arr)

Sharded arrays (v3 only)

from zarr.codecs import BloscCodec, BloscShuffle

writer = OMEZarrWriter(
    store="sharded_v3.zarr",
    level_shapes=[(1, 1, 16, 1024, 1024), (1, 1, 16, 512, 512)],
    dtype="uint8",
    zarr_format=3,
    chunk_shape=[(1, 1, 1, 128, 128),(1, 1, 1, 128, 128)],
    shard_shape=[(1, 1, 1, 256, 256), (1, 1, 1, 256, 256)],
    compressor=BloscCodec(cname="zstd", clevel=5, shuffle=BloscShuffle.bitshuffle),
)

writer.write_full_volume(
    np.random.randint(0, 255, size=(1, 1, 16, 1024, 1024), dtype=np.uint8)
)

Targeting Zarr v2 explicitly (NGFF 0.4)

import numcodecs

writer = OMEZarrWriter(
    store="target_v2.zarr",
    level_shapes=[(2, 1, 4, 256, 256), (2, 1, 4, 128, 128)],
    dtype="uint8",
    zarr_format=2,  # write NGFF 0.4
    compressor=numcodecs.Blosc(
        cname="zstd", clevel=3, shuffle=numcodecs.Blosc.BITSHUFFLE
    ),
)

writer.write_full_volume(
    np.random.randint(0, 255, size=(2, 1, 4, 256, 256), dtype=np.uint8)
)

Writing to S3 (or any fsspec URL)

# Requires creds for private buckets; public can be anonymous
writer = OMEZarrWriter(
    store="s3://my-bucket/path/to/out.zarr",
    level_shapes=(1, 2, 8, 2048, 2048),  # single level (TCZYX), no pyramid
    dtype="uint16",
    zarr_format=3,
)

writer.write_full_volume(
    np.random.randint(0, 65535, size=(1, 2, 8, 2048, 2048), dtype=np.uint16)
)

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Writer Utility Functions

multiscale_chunk_size_from_memory_target(level_shapes, dtype, memory_target) -> list[tuple[int, ...]]
Suggests per-level chunk shapes that each fit within a fixed byte budget.

• Works for any ndim (2…5).
• prioritizes the highest-index axis first (grow X, then Y, then Z, then C, then T).

Example: 16 MiB budget on large pyramids (rightmost-axis first)

from bioio_ome_zarr.writers.utils import multiscale_chunk_size_from_memory_target

# 4D (C, Z, Y, X) across 5 levels
level_shapes = [
    (8, 64, 4096, 4096),
    (8, 64, 2048, 2048),
    (8, 64, 1024, 1024),
    (8, 64,  512,  512),
    (8, 64,  256,  256),
]

# 16 MiB target
chunks = multiscale_chunk_size_from_memory_target(level_shapes, "uint16", 16 << 20)

chunks = [
   (1,  1, 2048, 4096),
   (1,  2, 2048, 2048),
   (1,  8, 1024, 1024),
   (1, 32,  512,  512),
   (2, 64,  256,  256),
 ]

add_zarr_level(existing_zarr, scale_factors, compressor=None, t_batch=4) -> None Appends a new resolution level to an existing v2 OME-Zarr store, writing in time (T) batches.

• scale_factors: per-axis scale relative to the previous highest level (tuple of length 5 for T, C, Z, Y, X).
• Automatically determines appropriate chunk size using multiscale_chunk_size_from_memory_target.
• Updates the multiscales metadata block with the new level's path and transformations.
• Example:

from bioio_ome_zarr.writers import add_zarr_level
add_zarr_level(
    "my_existing.zarr",
    scale_factors=(1, 1, 0.5, 0.5, 0.5),
    compressor=numcodecs.Blosc(cname="zstd", clevel=3, shuffle=numcodecs.Blosc.BITSHUFFLE)
)

Using Config Presets

Config presets make it easy to get started with OMEZarrWriter without needing to know all of its options. They inspect your input data and return a configuration dictionary that you can pass directly into the writer.

Visualization preset

The visualization preset (get_default_config_for_viz) creates a multiscale pyramid (full resolution plus downsampled levels along Y/X) suitable for interactive browsing.

import numpy as np
from bioio_ome_zarr.writers import (
    OMEZarrWriter,
    get_default_config_for_viz,
)

data = np.zeros((1, 1, 4, 64, 64), dtype="uint16")

cfg = get_default_config_for_viz(data)
writer = OMEZarrWriter("output.zarr", **cfg)
writer.write_full_volume(data)

This produces a Zarr store with the original data and additional lower-resolution levels for visualization.

Machine learning preset

The ML preset (get_default_config_for_ml) writes only the full-resolution data, chunked to optimize for patch-wise access often used in training pipelines.

Editing Zarrs

bioio-ome-zarr provides a utility for editing metadata of an existing OME-Zarr store in-place without rewriting image data.

The function:

from bioio_ome_zarr.writer import edit_metadata

allows you to modify common metadata fields such as:

• Image name
• Channel metadata
• Rendering definitions (rdefs)
• Axis names, types, and units
• Physical pixel size (with automatic pyramid propagation)
• Root-level coordinate transforms
• Creator / provenance information (NGFF v0.5)

Changing Axis Metadata (e.g. ZTX → TYX)

Sometimes an image was written with incorrect or placeholder axis metadata. For example, you may have a dataset whose axes were labeled as:

Z, T, X

but the data actually represents:

T, Y, X

You can correct the axis metadata in-place:

edit_metadata(
    "my_image.ome.zarr",
    axes_names=["t", "y", "x"],
    axes_types=["time", "space", "space"],
    axes_units=["second", "micrometer", "micrometer"],
)

⚠️ Important: This operation updates metadata only.

If the actual array order needs to change (for example, true ZTX data must become TYX data), you must rewrite the array data before updating metadata.

Updating Physical Pixel Size

To change the physical pixel size of the base resolution:

edit_metadata(
    "my_image.ome.zarr",
    physical_pixel_size=[1.0, 1.0, 0.5, 0.108, 0.108],
)

This will:

• Update the base resolution scale
• Automatically propagate scale changes to all pyramid levels
• Preserve relative downsampling ratios

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Updating Channel Metadata

Channel metadata is written into the OMERO metadata block.

from bioio_ome_zarr.metadata import Channel

channels = [
    Channel(label="DAPI", color="#0000FF"),
    Channel(label="GFP", color="#00FF00"),
]

edit_metadata(
    "my_image.ome.zarr",
    channels=channels,
)

Setting Creator Metadata (NGFF v0.5)

For NGFF v0.5 stores:

edit_metadata(
    "my_image.ome.zarr",
    creator_info={
        "name": "bioio-ome-zarr",
        "version": "3.1.0",
    },
)

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Notes

• The Zarr store is modified in-place.
• No image data is rewritten/rechunked.

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Issues

Click here to view all open issues in bioio-devs organization at once or check this repository's issue tab.

Development

See CONTRIBUTING.md for information related to developing the code.