How to measure single cell intensity in Qupath

I am Qupath user. And I wanna export the single cell intensity from my multiplexed image. I am not sure detection measurements table show the intensity or cell count ?
Can anyone help?

The detection measurement table shows all of the measurements that are listed at the top of the columns. The cell count would be the number of rows (minus 1 for the header).

As long as measurements were turned on during cell creation, each channel should have several single cell intensity measurements.

You may have to scroll across pretty far to find the one you want, though the Measurement Exporter helps take care of that by allowing you to populate the export with only certain values.

https://qupath.readthedocs.io/en/latest/docs/tutorials/exporting_measurements.html?highlight=export%20measurement#via-the-measurement-exporter

Thanks for your information. I wanna do single cell analysis like tsne or PCA from multiplexed image. So I want the columns which include markers and rows will be the intensity of specific marker.

Is it possible to have intensity from colocalization of two channels after I classified with single measurement classifier?

The measurements in the exported CSV file are the ones that are “in” the cell when the file is exported. If you calculate colocalization values between channels, then those values will be there. Pearson’s and Manders are not calculated by default. Looking in the Detection measurements or selecting a single cell and scrolling through it’s measurement list will show you what is available by default.

Colocalization is also a very generic word and can mean many different things, often other than colocalization. https://youtu.be/P2JvFe0hB_M?t=208
Are you looking for co-expression (basically the default measurements) or something else?

tSNE, PCA, PHATE, using QuPath exports etc are covered here:

Other software should work just as well as long as the files are formatted correctly.