Posted by
MRivers on
Sep 08, 2015; 4:25pm
URL: http://imagej.273.s1.nabble.com/FIJI-Plugin-tp5014267p5014270.html
I think the current convention is files like the GSETomo one should have the .ijm (ImageJ Macro) extension rather than .txt. I have tried that and the results are the same. It does not show up in the plugins menu either before or after doing Install Plugin.
Note that the netCDF is not actually yielding a binary image. It is interpreting your data as unsigned 16-bit integers, while it is actually signed 16-bit integers. What the GSETomo macro does is some operations to get the netCDF data to display correctly as signed 16-bit integers.
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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