Posted by
Krs5 on
Jan 29, 2016; 9:27am
URL: http://imagej.273.s1.nabble.com/simple-thresholding-problem-tp5015481p5015484.html
Dear Thomas,
I got better results using the macro code:
run("Subtract Background...", "rolling=50");
run("Bandpass Filter...", "filter_large=40 filter_small=3 suppress=None tolerance=5 autoscale saturate");
run("Auto Local Threshold", "method=Median radius=15 parameter_1=0 parameter_2=0 white"); // this uses the Auto Local Threshold plugin
run("Watershed");
run("Analyze Particles...", "size=10-Infinity add");
Kees
Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Gensch, Thomas
Sent: 29 January 2016 08:38
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]
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html