Hi, Im trying to use a plugin from ImageJ (Tubeness) in an existing workflow which does a nicer job of processing mitochondrial networks in my images (segmentation is much better than with either a tophat, or the enhance neurites feature of ‘enhanceOrSupressFeatures’), so I really do need this plugin (or to re-code it in python)…
But… Its been very intermittent getting it to work, and now its not working at all. Im sure its a Java environment problem an not a cellprofiler issue per se, but perhaps someone has a solution…
Let me explain my setup. On my winXP 64 workstation, at first, as the Tubeness plugin is not in the imageJ version provided with cellprofiler, I changed the path in the cellprofiler preferences for imagej plugins to point to the FIJI plugins folder (tubeness is in the VIB_.jar in /plugins in FIJI).
On my workstation this got things working for a while, I could load up cellprofiler with the macro below in the runImageJ module:
and get back the output of Tubeness ready for further steps in Cellprofiler. I could also execute Tubeness manually through the imageJ interface (open IJ interface with show button in the cellprofiler module, open an image, and execute tubness plugin).
So this was intially looking good, during a few days I had run on a few images and cleaned up the rest of the workflow. I had even shut down the workstation, installed cellprofiler analyst, done some other updates etc.
However, my attempts to get the same exact CP workflow to run on a different machine has failed - eg on windows server 2003. On the other machine, I could see the plugins in the plugin menu, I could run the plugin on an image, and get the first menu to set the Tubeness parameters, but after ok there is the error:
'Plugin or class not found: “Tubeness_”
Now, I also got a bit fancier with IJ macro batch mode and tried to clear memory (I’m describing everything incase it has an impact…)
However, today I started running into various problems.
First I was getting back a weird image from the ‘runImageJ’ step, the image was dark with only about 4 grey levels, so subsequent segmentation with CP was really off. The imageJ macro was running though… Now, I got around this problem when I chose not to ‘hide all windows on run’, & removed from the macro the lines ‘BatchMode’, and the GC step.
As I wanted the results, I started running over a full experiment (45 images) - closing IJ windows as I could - I got 90% through then IJ was out of memory.
Now the worst part. Since the out of memory, I have completely lost the ability to run the tubeness plugin from the CP imageJ on my workstation. I’m now in the same situation as on the windows 2003 server. I tried many many things, rebooting, re-point8ing to the Fiji/plugins folder, runing Fiji at the same time, copying the plugins folder from Fiji to /cellprofiler/plugins , copying also the plugins to /cellprofiler/imageJ/plugins nothing has worked…
the classpath from the IJ|plugins|utilities|ImageJ properties is:
java.class.path: C:\Program Files (x86)\CellProfiler\bioformats\loci_tools.jar;C:\Program Files (x86)\CellProfiler\imagej\ij.jar;C:\Program Files (x86)\CellProfiler\imagej\imglib.jar;C:\Program Files (x86)\CellProfiler\imagej\javacl-1.0-beta-4-shaded.jar
but that classpath was the same before when Tubeness worked!
thanks in advance if any one can help!