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:

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.

Activate the environment and install EuBI-Bridge via pip:

conda activate eubizarr
pip install --no-cache-dir eubi-bridge==0.1.3

ℹ️ Linux users: the graphical interface needs Qt's system libraries, which pip does not install. If eubi-gui stops with libEGL.so.1: cannot open shared object file, install them with sudo apt install libegl1 libgl1 libxkbcommon-x11-0 libdbus-1-3 libxcb-cursor0 (Debian/Ubuntu), or add pyqt6 to the mamba create command above so conda supplies them. The eubi command-line interface works without them.

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.