thresholding for analyze particle on uneven background

[saccente]

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[saccente]

ps I'm working with 8-bit images of course,don't care about colors

[Emanuele Martini]

I think that you can search for some top-hat filtering, if i remember well could be useful to remove uneven illumination background
http://it.mathworks.com/help/images/ref/imtophat.html

I don't know if exist some already exissting FIJI plugin that does that, but maybe yes.
Have a nice day,
Emanuele Martini