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

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

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

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

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.

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

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

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

Image data and Python scripts for the course on Bioimage analysis with Napari

CaMOS, a GUI for analysis of multimodal neuroscience datasets.