Particles and Background same color

[Arlamos]

Hello,

I am having a tough time separating my target particles from the material they are embedded in. I am trying to isolate the neurons, which are the white, sometimes gray spheres from the white/gray matter, which is the large blob of grayish material. The problem is that some of the neurons are not so much white as they are gray and match the unwanted areas, so that thresholding doesn't isolate them. If anyone knows of a way to approach this it would be greatly appreciated.

[JamesNYC]

I was able to improve it a little by using Photoshops "smart blur" command (adjusting settings to optimize getting rid of the grain in your image without losing too much detail).

Then I went to imageJ and thresholded

Another thing that might help on some of these images is:
Use the process >> subtract.
I downloaded your image and did it with a 30px rolling ball radius and "light background" unchecked and it seemed to do a decent job.

Another trick (which I didnt try with your image) is to split the image into smaller tiles (can be done with Photoshop slice tool and then save for web and devices). By thresholding localized areas of an image, you can set it to a level appropriate to the background in that section. Import all the tiles as a stack for convenience.

I just figured out this stuff recently for a project I am working on, so if it's bad advice please accept my apologies.. it's working for me at the moment though!