IF_Cell distance measurement

Dear All,

I never used Qupath for IF. I have 2 questions regarding qupath analysis :
Is it possible to identify and quantify cells which is stained with 2 different antibodies (I guess yes) ?
Is it possible to measure distance between 2 cell populations (stained with 2 different antibodies)?
How can we do it ?
Thanks for your reply !

Currently any nearest neighbor analysis that cannot be done with clustering can be done in R, after you export the Detections list (which come with X,Y coordinates).
saveDetectionMeasurements() works in the same way that the annotations version does, see elsewhere on the forums.

As far as quantifying and classifying, see here. Standard warnings about cytoplasmic stain apply.

I have been playing around with some ideas for NN analysis, but haven’t written any scripts yet. It is fairly straightforward in R (entire modules devoted to it), so there hasn’t been a huge need.

If you can classify an area (like tumor), you can use the distance transform function in 0.2.0m2 to find the distance of a cell type from the tumor annotation.

Thanks for the quick and clear reply!

Regarding my first question. Getting the detection measurement table is not issue. However, I don’t really understand what would be the suitable method te define the cut-off positivity for each channel.
how would you recommand me to do it ?

Generally with a negative control, such that your threshold picks up very little in the negative. That information has to be verified in some other way, either biologically or with some knowledge of how the staining could look. Too many different antibodies, markers, etc have different degrees of background or staining patterns to determine a one size fits all threshold method.