Open-source tools for biological image analysis and microscopy.
We maintain popular extensions for QuPath, including deep-learning segmentation (Cellpose/Omnipose), image registration (Warpy), spot detection (Spotiflow), and brain atlas integration (ABBA). Browse them all in our extension catalog.
Wrappers to call Cellpose, Elastix & Ilastik from Fiji, pyramidal image conversion with KHEOPS, label ↔ ROI conversion, Fourier Ring Correlation, an Imaris–Fiji bridge, and more.
ABBA registers 2D brain sections onto 3D reference atlases, with a Python interface and QuPath integration.
Tools for large multi-dimensional datasets: image loaders, visualization tools, and a fast CZI reader.
Point tracking with CoTracker3.
Materials for our Image Processing & Analysis MOOC, a colocalization board game, and reusable educational figures.
We welcome issues, pull requests, and questions on any of our repositories. Most projects are open-source.
