Posted by
Majurski, Michael Paul (Fed) on
Aug 18, 2016; 1:47pm
URL: http://imagej.273.s1.nabble.com/Segment-phase-contrast-image-tp5017034p5017055.html
Laurent,
Did you try to use the compiled version of Fogbank running with an MCR? Or did you run from source?
Both the executable and the source should be available at:
https://isg.nist.gov/deepzoomweb/resources/csmet/pages/fogbank_segmentation/fogbank_segmentation.htmlI you have not tried the source version it is more likely to work. I usually refer people to the compiled version since not everyone has a matlab license.
If you are having matlab compiler problems w.r.t. the mex files, none of those are required. They are only run if the mex64 file exists. The equivalent basic matlab code is included and it checks whether the mex file exists before trying to launch it.
Given that mex file versions are very finiky, I would suggest either recompiling the mex64 files from the .c source files, or simply deleting them and letting it run basic matlab code. There is basic matlab code included and it only runs the mex file if it can find it. If the mex files appear to be the problem, and you are not comfortable recompiling them from the included .c files, simply delete the .mex64 files and the code will run using basic matlab (albeit slower).
As for how to segment, there is a basic guide in the doc folder of the source code which is a good place to start for using the tool.
~Michael Majurski
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Laurent Guerard
Sent: Thursday, August 18, 2016 07:27
To:
[hidden email]
Subject: Re: Segment phase contrast image
Hi Michael,
Thanks for the segmentation link it worked very nicely. I now have delimited what is background and what is foreground.
Do you have any guidance on that watershed based on pixel intensity ?
I tried installing and running the matlab code but i'm having problems with compiler (My matlab seems to be too recent and it doesn't work with version 9 of the compiler)
Thanks again for your help.
Laurent
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