Note: Versions of QuPath
The following is a collaboration with Johanna Dela-Cruz, intended to make breaking into multiplex (multiple channel) image analysis just a little bit easier. The information presented will consist of a short video produced by Johanna and hosted on her YouTube channel, paired with a text description including example code and finer details written by me.
The project was created according to the steps shown in the official documentation (create folder, drag and drop images).
For another live example of performing multiplex analysis with QuPath, see Sara McAdle's presentation on YouTube from the 2023 From Samples to Knowledge , held in San Diego at the La Jolla Institute for Immunology.
A Zipped file containing a sample project you can use to test and follow along can be found in the same place as the scripting demo. In the “Multiplex demo” zip file, you will find two folders, one containing the images and a second containing the project along with the full scripts for the analyses shown (in Automate->Project scripts…)
Image of project tab in QuPath
This guide is certainly not the only way to run a multiplex analysis - and it contains many opinions that not everyone might agree with or might not apply to your specific project - but hopefully it includes enough suggestions and good practices to get a few people started. Validation is always important - testing different settings on your full data set, finding one that gives the results you want, and then calling that your analysis is the sort of thing that leads to retractions in the future. Not how good science works - in fact, running through your full data set repeatedly is more like a retrospective study, as the images have already been collected and you can run a multitude of analyses on them until you obtain your desired results.