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

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

Implementations of U-Net, Siam U-Net, U-Net++ and 3D U-Net for biological image segmentation

cytoscan

An offline Python microscopy perception tool for Sun research lab.

deepflash2

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

cytomine-python-client

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

faser

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

sarc-asm

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

clesperanto

A graphical user interface for clesperanto based on napari

magellanmapper

3D atlas analysis and annotation

napari-j

A plugin to exchange data with FIJI and to use FIJI image analysis from napari

napari-philow

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

run-stardist

Train and use StarDist models