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

OME-Zarr Converters Tools Architecture

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

Metadata

Release files for ome-zarr-converters-tools 1.1.1

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Source distribution (sdist)

Source distribution for ome-zarr-converters-tools 1.1.1
File	Size	Uploaded
ome_zarr_converters_tools-1.1.1.tar.gz	27.1 MB	Oct 15, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for ome-zarr-converters-tools 1.1.1
File	Interpreter	ABI	Platform	Reset
ome_zarr_converters_tools-1.1.1-py3-none-any.whl 93.2 kB Oct 15, 2026	Python 3	none	any	Details

Total release size: 27.2 MB

Release files / ome_zarr_converters_tools-1.1.1.tar.gz

Download URL	ome_zarr_converters_tools-1.1.1.tar.gz
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Release files / ome_zarr_converters_tools-1.1.1-py3-none-any.whl

Download URL	ome_zarr_converters_tools-1.1.1-py3-none-any.whl
Size	93.2 kB
Tags	Python 3
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Upload date	Oct 15, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/BioVisionCenter/ome-zarr-converters-tools
Publishing commit: github.com/BioVisionCenter/ome-zarr-converters-tools/tree/33cf8a2cc0963bb7cd5d6914d1f03554a15834f3

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Publishing configuration: github.com/BioVisionCenter/ome-zarr-converters-tools/blob/33cf8a2cc0963bb7cd5d6914d1f03554a15834f3/.github/workflows/ci.yml
Publishing logs: github.com/BioVisionCenter/ome-zarr-converters-tools/actions/runs/38772300677/attempts/1

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Subject: ome_zarr_converters_tools-1.1.1-py3-none-any.whl
SHA-256 checksum: b442fd4565c9800446faac669001d4732c6959c9aaf49ca28b5a0b73033c44f8 Verifying attestations