Re: counting cells in confocal images

Posted by leonliev on Jun 07, 2011; 9:06pm
URL: http://imagej.273.s1.nabble.com/counting-cells-in-confocal-images-tp3684340p3684342.html

Bruce, thanks a lot, this is great help! I should be able to play around with this and tweak some settings into a functional macro. most optimal situation would be to make one macro that would analyse everything, but if that isnt possible, at least i can get most work automated this way.

we use a leica sp5 confocal multiphoton setup. It spits out files in its own las format, which is a pain in the *** to work with, but we can retrieve tiff files from it, so thats fine. we can easily split for rgb as well. i honestly have no idea if there are better export options from las af software, ill check this out.

I hope I get it correctly that you suggest not splitting the channels for threshold (low\mid\high pos cells), but let particle analysis measure intensity and sort it out in excell? for particle analysis, is the range 70-400 and 0.8-1.0 circularity a standard setting you use? is this a setting that accepts like 95-99% of all normal cells? range is (i guess) dependant of the size of your image as well, right?

and last, does anybody have experience with nuclei counter in comparison to particle analyser? pros and cons?

anyway, everybody thanks a bunch for the help!