Multiple Cell Detections in same image

Hi All,

I am new to QuPath - Is there a way to convert detected objects into a new annotation object? I ran a cell detection and need to change the parameter for a subset of detected cells. I have them classified as a separate class, but its all within the same parent annotation. How to make all of the detected objects within a class a “new” parent annotation?
Thank you
Alan

Could you elaborate on what you want?

In the Sample scripts in the Automate menu, there is an option to create annotations from ROIs (which could be detected objects.

In the points tool, there is an option to turn all cell detections into point annotation objects. You could remove all of the other classes so that only the cells you wanted to convert into points remained, and then add the other classes back afterwards.

Pete wrote a script that destroys all cell detections and creates an annotation where they used to be, based on the class of the nearest detection. I forget what version of the software it was for, though, and you haven’t specified what you are using.

If you are comfortable scripting, you might also be able to create an annotation ellipse of “some size” around each of a certain class of cell, then merge them into a single annotation.

Thanks, this is helpful. I am trying to come up with a simple nuclear segmentation (IF) but need to run different parameters of cell detection as some cells are merged together (or close together) and need alternate parameters.