README.md

QuPathNotebooks

Jupyter notebooks for teaching QuPath - Feb 2025, QuPath v0.6.0rc3
Hosted by The Microscopy and Histology Core Facilities at La Jolla Institute
Sara McArdle
Zbigniew Mikulski
Assisted by
Michael Nelson of LOCI

Join Slack!

Prepare for the workshop

Introductory video

Please watch this short video which introduces some QuPath concepts and has some information on installation issues.

Version of QuPath we will be using: 0.6.0RC3

Make sure to install this ahead of time, as some companies/institutes/hospitals require administrator access to download and set up QuPath.
Get it here!

Download your images ahead of time!

Download the files from Google Drive

See steps 1 and 2 in Session 1 to create your first project! TODO ADD LINK

If you have time, watch this excellent introduction by the author of QuPath!

Or skip directly to the part discussing QuPath!

See you there and online!

Additional resources

Ask questions

https://forum.image.sc/tag/qupath

QuPath documentation for 0.5, the latest stable release

Main docs - https://qupath.readthedocs.io/en/0.5/
Scripting Javadocs - https://qupath.github.io/javadoc/docs/

Introduction to QuPath scripting (unofficial)

https://www.imagescientist.com/image-analysis

Useful plugins and associated software

Segmentation

https://github.com/qupath/qupath-extension-stardist
https://github.com/BIOP/qupath-extension-cellpose
https://github.com/qupath/qupath-extension-instanseg

Aligning images

https://github.com/qupath/qupath-extension-align
https://imagej.net/plugins/bdv/warpy/warpy-image-combiner

Python access

https://github.com/Bayer-Group/paquo

Interesting reading - imaging and analysis

Start Here
Introduction to Bioimage Analysis
Workflows and Components of Bioimage Analysis
A biologist’s guide to planning and performing quantitative bioimaging experiments

General
Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions
Developing open-source software for bioimage analysis: opportunities and challenges Open-source deep-learning software for bioimage segmentation
The QuPath community

Do good things, not bad things!
Avoiding a replication crisis in deep-learning-based bioimage analysis
Avoiding Twisted Pixels: Ethical Guidelines for the Appropriate Use and Manipulation of Scientific Digital Images
Imaging methods are vastly underreported in biomedical research
Reproducibility standards for machine learning in the life sciences

Acknowledgements

La Jolla Institute Core facility staff IT Coordinaters CZI funding Research group of Pete Bankhead