Bioimage Analysis Python Packages

stardist

StarDist - Object Detection with Star-convex Shapes

partseg

Tool for segmentation in bioimaging

bioimageio-core

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

faser

A python based toolkit for psf estimation using a vectorial model of the electromagnetic field

openhcs

Typed, reproducible high-content microscopy workflows across GUI, Python, CellProfiler, Napari/Fiji, GPU, and local MCP agents.

pyclesperanto-prototype

GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data

micro-sam

Segment Anything for Microscopy

scip

Scalable Cytometry Image Processing (SCIP) is an open-source tool that implements an image processing pipeline on top of Dask, a distributed computing framework written in Python. SCIP performs projection, illumination correction, image segmentation and masking, and feature extraction.

bio-image-unet

Implementation of U-Net, U-Net++, and 3D U-Net in PyTorch for analysis of bio-images

sarc-asm

A Python package for AI-based comprehensive analysis of sarcomere structure and function in cardiomyocytes

omnipose

Omnipose: a high-precision solution for morphology-independent cell segmentation

zenreg

ZenReg is a Python-based high-throughput, memory-efficient pipeline for N-dimensional image registration, designed for large microscopy and imaging datasets.

deepflash2

A deep-learning pipeline for segmentation of ambiguous microscopic images.

ome-zarr-pyramid

Read, write and downscale OME-Zarr (NGFF) pyramids with a lazy, memory-bound Pyramid object

omio-microscopy

OMIO is a Python library for reading, organizing, merging, visualizing, and exporting multidimensional microscopy image data under explicit OME-compliant axis and metadata semantics.

cytomine-python-client

A web platform for collaborative analysis of very large bio-medical images

cytoland

computer vision models for single-cell phenotyping

viscy-utils

computer vision models for single-cell phenotyping

viscy-models

computer vision models for single-cell phenotyping

viscy-transforms

computer vision models for single-cell phenotyping

viscy-data

computer vision models for single-cell phenotyping

cytoscan

An offline Python microscopy perception tool for Sun research lab.

clesperanto

GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data

magellanmapper

MagellanMapper is a graphical interface for 3D bioimage annotation, atlas registration, and regional quantification