bioimage

A Python-based tool for parallelized conversion of image datasets from various formats to OME-Zarr, with support for distributed processing and multi-dimensional concatenation.

A nextflow based tool that wraps bfconvert and bioformats2raw to convert image data collections to OME-TIFF and OME-Zarr, respectively, in a parallelised manner.

Clear multiscale image metadata manipulation in python

A lightweight library for lazy operations on Zarr arrays without task graph overhead

Tired of counting cells by hand? 🔬 This project uses a U-Net deep learning model to automatically find and count cells, saving you time and improving accuracy. Perfect for researchers and bio-AI enthusiasts!

Lazy, memory-bounded connected-components labeling for large N-dimensional arrays (interior-boundary reconciliation; dask output)

A specialized batch-processing pipeline for Zeiss CZI files. Optimized for ApoTome & Brain sections. Fixes hyperstack dimensions, recovers LUTs, and removes shading via rolling-ball pre-processing.

Lazy, memory-bounded connected-components labeling and per-object measurement for OME-Zarr pyramids