QuPath - Open-source bioimage analysis for research

StarDist - Object Detection with Star-convex Shapes

A vision-language foundation model for computational pathology - Nature Medicine

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

AI-based pathology predicts origins for cancers of unknown primary - Nature

This is the repository for a Python bioimage analysis course which establishes the fundamentals of image analysis in the context of biological imaging.

A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.

Fast and scalable search of whole-slide images via self-supervised deep learning - Nature Biomedical Engineering

A tool for cell instance aware segmentation in densely packed 3D volumetric images

Mastodon – a large-scale tracking and track-editing framework for large, multi-view images.

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

C++ library and command-line software for processing and analysis of terabyte-scale volume images locally or on a computing cluster.

computer vision models for single-cell phenotyping

SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.

Fiji plugin for object(s) detection using template(s) matching

ImageJ macros and scripts written at the imaging facility MRI

Tool for segmentation in bioimaging

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

Fast reconstruction of spatial networks from bioimages.

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