From Samples to Knowledge 2025 Repo#
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
and
Michael Nelson of LOCI
Ask questions in the image.sc forum thread!#
We ask that the majority of questions be directed to the image.sc forum thread here, where it will be easiest for all of the hosts to respond to questions and issues as they have time.
If you are interested in keeping up with the topic, make sure to create an image.sc forum profile, and set the post to “Watching” - which will send a notification email whenever there is a new post.
Prepare for the workshop#
Introductory video#
Please watch this short video which introduces some QuPath concepts and has some information on installation issues.
Install QuPath: we will be using: 0.6.0RC3#
Make sure to install QuPath ahead of time, as some companies/institutes/hospitals require administrator access to download and set up QuPath.
Get it here!
Download your data and scripts!#
If you wait until you arrive, you will be competing with everyone else for bandwidth!
Download the files from Google Drive
You must unzip your files before using them!
See steps 1 and 2 in Session 1 to create your first project!
Download the Warpy extension and InstanSeg models#
Install the Warpy extension into your copy of QuPath 0.6.0
Warpy download here
There will be a number of .jar files - drag them into an open QuPath window to install, or create an Extensions folder in QuPath’s Preferences Edit > Preferences > Extensions and place them in that folder.
Instructions for InstanSeg setup can be found by scrolling down to Method 2- One Time Setup, here.
If you have time, watch this excellent introduction by the author of QuPath!#
Or skip directly to the part of the video discussing QuPath!
See you there and online!#
Additional resources#
Ask questions (the devs check here)#
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)#
Useful plugins and associated software#
Segmentation
#
qupath/qupath-extension-stardist
BIOP/qupath-extension-cellpose
qupath/qupath-extension-instanseg
ksugar/qupath-extension-sam
Aligning images
#
qupath/qupath-extension-align
https://imagej.net/plugins/bdv/warpy/warpy-image-combiner
Python access
#
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
:heavy_dollar_sign: Multiplex protein imaging in tumor biology - review
Spatial analysis by current multiplexed imaging technologies for the molecular characterisation of cancer tissues
Video - Creating quality microscopy figures for manuscripts
Additional video on figure creation
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#
Peter Sobolewski, for helping convert this repo into a classier website/Gitbook!
Staff from the La Jolla Institute, including
Lisa Bouker, Admin Assistant Extrordinaire!
Zeynel Savari for AV and IT help
The LJI Facilities department
Funding: Chan Zuckerberg Initiative Imaging Scientist grant
Research group of Pete Bankhead