Identifying nuclei from an image with high cell density


#1

Hi,
I have an image with nuclei very close to each other (Image: https://files.fm/u/b9aqrdmh). I have rescaled the intensity and applied the threshold. The primary objects are being identified as clumps. Any suggestions? Is there a way of identifying primary objects using the module and then manually adding and editing objects as necessary? EditObjectsManually module does not allow me create objects and editing the boundaries also seems difficult by moving the circles.
Any help would be appreciated.

Thanks!


#2

I don’t have time to carefully engage with your images right now, so hopefully someone will be able to soon, but just fyi you CAN add objects in EditObjectsManually by just pressing the “F” key to freehand draw. I recommend looking carefully through that module’s help, there are definitely some tricks to speed up editing of objects with it (though obviously the best thing to do is get the segmentation right the first time!).

In general, playing with the declumping settings in IdentifyPrimaryObjects will be the best way to go- again, read through the module help for those options.