¶ Training resources
¶ QuPath YouTube channel
Channel dedicated to QuPath tutorials by the creator himself
¶ Installing QuPath & BIOP extensions
¶ BIOP introduction slides
¶ Official Documentation
- On the official documentation
- On the official website
¶ QuPath related tools and extensions
¶ StarDist
Cell segmentation using Deep Learning, custom implementation by Pete Bankhead
StarDist for QuPath
Main StarDist Repository
¶ Cellpose
Wrapper for calling a Cellpose installation within QuPath, handling large tiles
Cellpose for QuPath
Main Cellpose Repository
¶ CytoMap
Clustering tool for data crunching, with the possibility to import and export QuPath results
CytoMap
¶ PAQUO
Python layer interface for accessing QuPath Projects directly within Jupyter Notebooks or even interacting with QuPath via Python.
PAQUO
¶ BIOP Extension
A series of small quality of life methods to ease interaction with QuPath for the BIOP's User Projects
https://github.com/BIOP/qupath-extension-biop
¶ QuPath - OMERO
Reading images and sending annotations from OMERO
Extension written by the QuPath team - Documentation here
https://github.com/qupath/qupath-extension-omero
¶ QuPath - HRM
Sending images between QuPath and HRM
Extension written by the BIOP
¶ Warpy
Using BigDataViewer transformations to register and transform images and objects.
https://github.com/BIOP/qupath-extension-warpy
¶ ABBA
2D to 3D atlas registration
https://github.com/BIOP/qupath-extension-abba