Manually seeded nuclei segmentation/ Marker controlled watershed plugin

Posted by MrScientistman2 on
URL: http://imagej.273.s1.nabble.com/Manually-seeded-nuclei-segmentation-Marker-controlled-watershed-plugin-tp5014479.html

Hi all,


Here is what I am looking for:


I want to manually or semi-automatically mark the aproximate center of cell nuclei in 2D grey-scale images, then I want to find a plugin that could generate a segmentation of these nuclei, for example as ROIs in the ROI manager. Attached is an example image of nuclei that is similar to what I will be using. The end-goal is to measure the intensity of different antibody staining colors in individual nuclei (extra channels not in attached image).


It seems so hard to find a working plugin that takes MANUAL seed input!


Some options I've tried:


http://fiji.sc/Marker-controlled_Watershed

This plugin also claims to be fit for my problem, but I don't understand how it works. How should the marker input image be? Should it contain ROIs, 255-value pixels on a 0-value background, some RGB input markers or something else? It's really frustrating. Whatever I'm trying its just outputting a totally black image as the result.


http://imagej.nih.gov/ij/plugins/inserm514/Documentation/Watersheds_514_V2/Watersheds_514_V2.html

This plugin by Cutrona J. and Bonnet Noel seems to do excately what I want, but for some reason it doesnt work on my computer/ImageJ/FIJI. Is it due to not working on newer Javas or something?


Best wishes,

Anders


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