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

Solid Tumor Associative Modeling in Pathology

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

computer vision models for single-cell phenotyping

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

Tool for segmentation in bioimaging

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

Fast reconstruction of spatial networks from bioimages.

An introduction to OME-Zarr for big bioimaging data

Guides and code for 3D nuclear instance segmentation

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

A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources

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

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

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

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

Automated batch processing of tissue microscopy image data with a text-based interface