Bioimage Analysis Python Packages

stardist

StarDist - Object Detection with Star-convex Shapes

bioimageio-core

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

partseg

Tool for segmentation in bioimaging

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.

cytomine-python-client

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

bio-image-unet

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

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.

sarc-asm

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

deepflash2

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

faser

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

viscy-models

computer vision models for single-cell phenotyping

cytoscan

Cell migration analysis for microfluidic ATPS channels

viscy-data

computer vision models for single-cell phenotyping

viscy-transforms

computer vision models for single-cell phenotyping

magellanmapper

3D atlas analysis and annotation

clesperanto

A graphical user interface for clesperanto based on napari

napari-philow

Python-based Human-In-the-LOop Workflow: PHILOW is an interactive deep learning-based platform for 3D datasets

napari-j

Connect Napari with FIJI/ImageJ

run-stardist

Train and use StarDist models