Hi, I am using a multichannel cytof TIFF. From this, I use the brush tool to select the cells of interest. Then use cell detection to create an area around the nucleus to represent the cell.
I want to create a mask using my mitochondrial mass marker to then look at mitochondrial protein intensities in the same pixels as the mass marker within each cell.
I cant seem to get the colocalisation scripts to work. One alternative I found was using tile creation (1 pixel) then getting the data from this. However this is limited to annotations not detections so does not split for each cell but the area created by the brush tool.
Is there a way to
Create an image mask so only analyse pixels within each cell with mito mass value >1 (seems to be the background for my mass marker)
convert detections to annotations would be the alternative.
I am using Qupath 0.2 but have the older 1.2 installed as well. the images consist of 11 channels with mass marker on 5 and my nuclear markers on 10 and 11