Filter/Treshold to count small nuclei/Dapi

I am wondering if I can get some input on what is the best way to process this in order to to particle analysis. Appreciate some help. Thanks!
Dapi_Crop_Montage.Project Maximum (2.8 MB)


Can you be more specific about what exactly you want to measure?

You say ‘particle analysis’ - but can you be more explicit?

Perhaps you can start reading here (Particle Analysis page on the ImageJ wiki) to see if that can get you started.


I want to do a total count and measure area of each particle and total density. The trouble I am having is to apply filters and Threshold : I can’t figure out a way to get each nuclei separated, since some overlap.

Given the image you posted. I am not sure you will be able to effectively delineate each individual nuclei - they are quite dense. Even visually - it is difficult to distinguish individuals from one another because of the overlap and varying intensities - therefore, to do this computationally … it is most likely not possible.

You could however look at the overall population of cells … to examine the area. It just depends on your biological question. But again - I do not believe you will be able to separate your nuclei in this given dataset.