Bioimaging Python Packages

biomero

BIOMERO.analyzer - A python library for easy connecting between OMERO (jobs) and a Slurm cluster

bioimageio-core

Python libraries for loading, running and packaging bioimage.io models

iohub

Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata

ome-zarr-io

Write, read and validate OME-Zarr 0.5 images and high-content screen plates.

biomero-shallower

Python library and CPU-only container for shallow OME-Zarr normalization in BIOMERO. Reuses verified canonical pixels while retaining new and changed image and label data, reducing storage and result transfers. Shared by BIOMERO.importer and remote Slurm workflows; no OMERO connection or credentials required.

phenome

Dataset- and model-agnostic tool for phenotyping analysis using deep learning embeddings and image properties.

tiledb-bioimg

Package providing bioimaging functionality using TileDB. Source of the tiledb-bioimg Python package.

iscc-bio

ISCC Processing for Multi-Dimensional Bioimage Data

luxar

Compile and explore arbitrarily large n-dimensional scientific data in the browser — points, lines, Gaussian splats and meshes, streamed from Zarr and rendered on the GPU.

pyimc

Rust library for reading imaging mass cytometry (IMC) data stored in .mcd files.

macsima-qc

Quality control pipeline for MACSima / MACSiQView cell segmentation

napari-tiledb-bioimg

TileDB BioImaging plugin for Napari