Gallery including detected cells


#1

Hello,
we are interested in obtaining a gallery including the detected cells, cutting
the image regions that are likely to be the cells with the desired features.

Do you have sthg like that in mind for next releases of Cell Profiler?

Is there any module in the current release I could take advantage of?

Thank you very much.


#2

Hi,
Interesting idea! That would be fairly straightforward to implement - you would use the FilterByObjectMeasurement module to create the set of objects you care about, giving them a new name (like ‘FilteredObjects’). Their X Y locations will be automatically stored by the module, so all that remains is to write a module that asks the user for the name of the Objects they would like to montage and the size they would like to cut out around each X Y location (e.g. a 50 pixel-square region around each cell), the original image name from which the little cell images should be cut, and the name the user would like to call the resulting image. Your new module would cut the regions out and place them together into a new montage image, and the user could use SaveImages to save it.

We won’t be able to work on that for quite a while, so you are on your own! We would be happy to include it in the next release if you will contribute the code.

Cheers,
Anne