Posted by
Jeremy Adler on
Jan 29, 2016; 9:24am
URL: http://imagej.273.s1.nabble.com/simple-thresholding-problem-tp5015481p5015483.html
Try the various options in
Auto Local Threshold
the Phansalkar method is promising
After thresholding use the Watershed binary operation to separate overlapping objects. The generate ROIs for each object with Analyze Particles
Also
1) check your image acquisition for even illumination, you will need a slide with a uniform fluorescence - and correct for unevenness. To some extent the Local Thresholding methods deal with uneven illumination but getting the best images is always a good start and becomes important if you want to make the relative intensities independent of the objects position on the slide.
2) It is not clear what your images are but you may be able to add a transmitted light image or an autofluorescence image that has less variability between the objects but shows the same objects. These images might be easier to threshold
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Gensch, Thomas
Sent: den 29 januari 2016 09:38
To:
[hidden email]
Subject: simple thresholding problem
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:+49-2461-618068
Tel:+49-2461-614216
email:
[hidden email]
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