Removing false positive spots from Qupaths subcellular detections?

Hello everyone.

I have a problem regarding the subcellular detection in Qupath. Basically I have some fluorescence images with in-situ dots in 2 channels. My tissue samples are Lung with quite alot of auto-fluorescence, in combination with some weak signal I get several false positives with my subcellular detections.

The good news is that I have scanned an empty channel where auto-fluorescence is strongly detected. I can use “add intensity features” in my auto-fluorescence channel to add intensities to all my detections. Now I want to remove all subcellular detections with auto-fluorescence intensities above a certain threshhold and then update my cell-detections to the correct number of spots/cell.

Is this possible through a script? I saw Petes warning about adding/deleting spots but that is exactly what I want do do. I previewed my auto-fluorescence measurements and believe removing false positive detections based on the auto-fluorescence intensity should work fairly well.

Image:
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Detections:
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True Spot Intensities:
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False Spot Intensities:
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Should be possible with a script, though you will need to calculate new subcellular detection measurements for the parent cells. Guessing that is the warning from Pete, though.

Here are a bunch of scripts and descriptions for how to remove things. And you can make new measurements using the child objects for each cell using variants of these scripts. I’ll take a look in more detail later if I have time, but what you want to do is fairly straightforward.

In case I do have time to look at this later, it would be important to know which version of QuPath you are using. And if it isn’t M4/M5 or 1.2/1.3, you might be on your own :slight_smile:

I’m working in M5.

I’ll take a look at the links you sent and if I make some progress I’ll let you know. Thanks a lot for the help.