Segmentation of MPM in-vivo images of human skin

I have some problems to segment my images (stacks).
I need to do cell counting, measuring the nucleus (diameter) and the nucleus-cytoplasm ratio, preferably automatically to get reproducible results.
Here is a stack of images. I need to do the measurement above for all images.
I’m working with a MPM (multiphoton microscopy) and get 16bit images, the length is 207x207um and Pixel 512x512 per image.
I would be really happy if some got an idea, since i already watched some basic and specific tutorials about it, but always fail to segment my images.

Greetings from Germany

1_z010.tif (2.1 MB) 1_z009.tif (2.1 MB) 1_z008.tif (2.1 MB) 1_z007.tif (2.1 MB) 1_z006.tif (2.1 MB)

1 Like

Hey @Niklas,

I had a quick look at your images. Could you maybe draw on a screenshot what you want to segment/count/measure? How can one differentiate cells and nuclei?

I see these 20 objects on the left, but are the other objects around also of interest?


1 Like

Thank your for your fast reply! I choose a different picture for a better understanding and i drew on 2 different cells arrows. Arrows pointing to the black spot are showing the nucleus while the arrows pointing to the white surrounding are showing the cytoplasm of the corresponding cell.

Same applies for the image you had a look on. Black dots surrounding my white matter are cells.


1_z007-1.tif (512.5 KB)