StarDist - Object Detection with Star-convex Shapes

Vision-Language Pathology Foundation Model - Nature Medicine

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

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

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

Solid Tumor Associative Modeling in Pathology

computer vision models for single-cell phenotyping

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

Tool for segmentation in bioimaging

Fast reconstruction of spatial networks from bioimages.

Guides and code for 3D nuclear instance segmentation

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

An introduction to OME-Zarr for big bioimaging data

Collection of useful (to me) python scripts for interacting with napari

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

Track single cells and profile the cell cycle with PCNA fluorescence images

Lightweight segmentation toolkit for fine-grained and multi-part segmentation of grayscale 2D/3D images, with napari support.

Automated batch processing for tissue microscopy image data

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.

Create a nice exploded visualization of segmented cells in a tissue.