Posted by
MRivers on
Sep 08, 2015; 4:40pm
URL: http://imagej.273.s1.nabble.com/FIJI-Plugin-tp5014267p5014271.html
I just renamed GSETomo_.txt to GSETomo.ijm.
I updated to the latest version of ImageJ (1.50b) in a normal ImageJ (not Fiji) installation. I put GSETomo.ijm in the ImageJ/plugins folder. When ImageJ starts up it shows GSETomo in the plugins menu. So it works fine.
I then did exactly the same thing with Fiji. GSETomo does not show up in the plugins menu. I also tried Plugins/Install Plugin and selected GSETomo.ijm. It reported that it was installed and told me to restart Fiji, but GSETomo still does not appear in the plugins menu. It appears that Fiji is not just ImageJ ☺
There must be some other trick required to get a macro to show up in the plugins menu in Fiji that is not required with regular ImageJ.
Mark
From: Anovitz, Lawrence {Larry} M. [mailto:
[hidden email]]
Sent: Tuesday, September 08, 2015 10:23 AM
To:
[hidden email]
Subject: FIJI Plugin
I am trying to load 3D X-ray CT images obtained at the APS into FIJI.
According to the APS website, this requires two files, labeled
GSETomo.txt and NetCDF_-3.jar
The description of both how the data are processed, and how to visualize it with ImageJ is at
http://cars9.uchicago.edu/software/idl/tomography.htmlUnfortunately, when I try to use FIJI’s Install Plugin feature it SAYS that GSETomo.txt has been installed, but
it does not show up under plugins, either immediately or after a restart.
Here is all that is in GSETomo.txt
run("Load NetCDF File");
run("XOR...", "value=1000000000000000 stack");
run("Calibrate...", "function=[Straight Line] unit=[Gray Value] text1=[0 65535] text2=[-32768 32767 ]");
run("Enhance Contrast", "saturated=0.5");
I am told this works on ImageJ, but not on FIJI, although I have not tried the former.
NetCDF does show up, and can be run, although it just yields a binary image.
Can anyone tell us how to fix this? Thank you.
—Larry Anovitz
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