Manual counts within objects

Hi. I have been using fast cell counts to count CD3 positive T-cells per tissue core for a large TMA project. I was hoping to be able to go back and manually “audit” a proportion of the cores using the count points tool for some sort of added validation. However when I do this the counted points are no longer associated with the parent object (detected tissue within the TMA core). So I can’t directly count points per mmsq of tissue core. Is there some simple solution to this (using version 0.1.2). Pathologist - not a computer scientist - so my knowledge of object hierarchies etc. is fairly rudimentary. Thanks.

Not sure what is happening here, but you should never get the number of child points within an annotation from the annotation measurement. You might want to do something like name the points after the Core, so that you can divide the correct list of points by the correct core area.



Alternatively, you can classify all of your manually annotated points and convert them into detections using a script.

Then they should show up in the detection list for the core/annotation and the density can be calculated similarly to other classes.

I am surprised you don’t directly compare the manual counts vs the positive counts, though, since the areas are the same.