EuBI-Bridge

EuBI-Bridge is a tool for distributed conversion of microscopic image collections to the OME-Zarr format (v0.4 or v0.5). It can run on the command line or as part of a Python script.

A key feature of EuBI-Bridge is aggregative conversion, which concatenates multiple images along specified dimensions—particularly useful for handling large datasets stored as TIFF file collections.

EuBI-Bridge is built on several powerful libraries, including zarr, bioio, dask-distributed and tensorstore, among others. Relying on bioio plugins for reading, EuBI-Bridge supports a wide range of input file formats.

Key Features

  • Parallelised batch conversion to OME-Zarr version 0.4 or 0.5 (with sharding)
  • Conversion with multi-dimensional concatenation
  • Distributed conversion on HPC clusters
  • N-dimensional chunking/sharding
  • N-dimensional downscaling
  • Options for displaying/updating pixel metadata

Installation

The following steps can be followed to install EuBI-Bridge:

  1. Create a conda environment with the required dependencies:

    mamba create -n eubizarr openjdk=11.* maven python=3.12
    ℹ️ Specify either python=3.11 or python=3.12. EuBI-Bridge is currently only compatible with Python 3.11 or 3.12 due to conflicting dependencies. We are working on supporting a wider range of Python versions in future releases.

  2. Activate the environment and install EuBI-Bridge via pip:

    conda activate eubizarr
pip install --no-cache-dir eubi-bridge==0.0.7b3

Additional Notes

  • EuBI-Bridge is in the beta stage, and significant updates may be expected.
  • Community support: Questions and contributions are welcome! Please report any issues.