QuPath Spatial analysis - getting started

I am a Pathologist and have enjoyed using QuPath for several months and slowly mastering cell detection, classifiers etc. Now that I want to move on to spatial analysis - I’m finding it harder to make any progress. An example of what I would like to do is

  1. create measurements (and ?image overlay) of single DAB positive lymphoid marker eg stromal CD8 distance to tumour cells and 2. is it possible to create concentric partitioning rings around tumour islands to calculate immune cell density at different distances from the edge of the tumour cells ? I’ve been pouring over other posts and tutorials etc but cant seem to find what I need.
    many thanks.
    E

Hi!

Spatial analysis can mean many different things, including cluster and hotspot analysis, which I have been interested in!


For your specific problem, I could see two ways to go about it. Both involve being able to define the border of your tumor region with an annotation, and then use Objects->Annotations->Expand annotations.
The first way would be as described, creating concentric rings (you can do this by selecting Remove interior for one ring, it gets more complicated if you want to do more).
image

An easier way might be to define the maximum range you are interested in, create a single expansion (while removing the interior), and then use Analyze->Spatial analysis->Distance to annotations 2D. If your tumor annotation has a class (like Tumor), that will calculate the distance of all cells to any annotation with a “class”. Then, you would take all of the cells within the tumor expansion area, and calculate the mean value for the “Distance to Tumor” measurement, summing up all of the distances and dividing by the number of cells.

Feel free to ask if you want any elaboration on any of those points.

many thanks fo that Mike I’ll give it a try
regards
Ewan

2 Likes