simple thresholding problem

Posted by Gensch, Thomas on Jan 29, 2016; 8:38am
URL: http://imagej.273.s1.nabble.com/simple-thresholding-problem-tp5015481.html

dear all,

i have a (rather simple?) problem of identifying circular and elliptical objects in a fluorescence image (see the attached sample picture). i want to generate a mask, that i can use in a second image (different fluorophore and color, different structures) to select the interesting areas.

while by eye and freehand drawing one can nicely mark the limits of the object, with all the thresholding tools in imagej (i tried "threshold in "adjust" and the "autothreshold plugin") i obtained only mediocre results (one of the best examples is attached). i can see the problem (in some parts due to close localization and very different fluorescence intensities by neighbouring objects the space between objects has intensity values larger than some of the weaker fluorescent elliptical objects.

i wouId appreciate very much, if one of  you could help me or suggest a better approach,

thanks a lot,


thomas


Dr. Thomas Gensch
Institute of Complex Systems 4 (ICS-4), Cellular Biophysics/Institut fuer Komplexe Systeme 4, Zelluläre Biophysik
Forschungszentrum Juelich (Research Centre Juelich)
52425 Juelich
Tel:[phone]
Tel:[phone]
email: [hidden email]


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