ome-zarr-converters-tools
A Python library that provides shared utilities for building OME-Zarr image converters. It handles tile management, image registration, filtering, validation, and writing OME-Zarr datasets.
Features
- Abstraction layer for building OME-Zarr images and HCS plates from microscope metadata and image data
- Customizable pipeline for filtering, validating, registering, and tiling images
- Python API for building custom converters, with optional Fractal integration for parallel processing
- Flexible input: parse tiles from DataFrames or construct them programmatically
Architecture Diagram
Getting Started
Install via pip:
pip install ome-zarr-converters-tools
For converting data stored on S3 (s3:// URLs), install the s3 extra:
pip install "ome-zarr-converters-tools[s3]"
Quickstart
Convert a tiles table (one row per tile: stage position, size, and image file) into a single OME-Zarr image:
import pandas as pd
from ome_zarr_converters_tools import (
AcquisitionDetails,
AutoTiling,
ChannelInfo,
ConverterOptions,
OverwriteMode,
StagePositionCorrections,
WriterMode,
build_default_registration_pipeline,
single_images_from_dataframe,
tiled_image_creation_pipeline,
tiles_aggregation_pipeline,
)
acq = AcquisitionDetails(
channels=[ChannelInfo(channel_label="DAPI")],
xy_pixel_size=0.65, # micrometers
z_spacing=1.0,
)
tiles = single_images_from_dataframe(
tiles_table=pd.read_csv("tiles.csv"), acquisition_details=acq
)
options = ConverterOptions()
tiled_image = tiles_aggregation_pipeline(
tiles=tiles, converter_options=options, resource="/path/to/image/files"
)[0]
tiled_image_creation_pipeline(
zarr_url="/path/to/output.zarr",
tiled_image=tiled_image,
registration_pipeline=build_default_registration_pipeline(
StagePositionCorrections(), AutoTiling()
),
converter_options=options,
writer_mode=WriterMode.BY_FOV,
overwrite_mode=OverwriteMode.NO_OVERWRITE,
resource="/path/to/image/files",
)
See the tutorials for HCS plates, custom image loaders, and Fractal tasks.
Documentation
For detailed documentation, tutorials, and API reference, visit the official documentation.
The documentation includes:
- HCS Plate Tutorial -- converting plate-based microscopy data
- Single Images Tutorial -- converting standalone images
- Advanced Tutorial -- programmatic tile construction with custom loaders
- Fractal Tasks Guide -- building parallel converters with the Fractal platform
- Pipeline Configuration -- filters, registration, tiling, and writer modes
- API Reference
1 maintainer
Metadata
1 maintainer
Release files for ome-zarr-converters-tools 1.1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| ome_zarr_converters_tools-1.1.0.tar.gz | 27.1 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| ome_zarr_converters_tools-1.1.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 27.1 MB
Release files / ome_zarr_converters_tools-1.1.0.tar.gz
| Download URL | ome_zarr_converters_tools-1.1.0.tar.gz |
|---|---|
| Size | 27.1 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
39bc0186a094938f682d6d065e8fe3d998dfee9c632ed2faad1429a50b02783e
|
|
BLAKE2b-256 checksum How to use checksums |
115bfe79b73bd8617cf94fee5e4439e3740cd15543e924aa4b1e0f03661e835b
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 15, 2026.
Transparency logRelease files / ome_zarr_converters_tools-1.1.0-py3-none-any.whl
| Download URL | ome_zarr_converters_tools-1.1.0-py3-none-any.whl |
|---|---|
| Size | 88.2 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
116ba64bd7a9689faaf2b9440ef12768b99ab4aaeeb935124d4838989f9a7aba
|
|
BLAKE2b-256 checksum How to use checksums |
453b84f71e5b6517130e31cdc2e578e1988ce6382e2e31f244aff90b94b2502e
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 15, 2026.
Transparency log
