Results Table in Batch Processing

Posted by Kidd, Mary on Aug 13, 2014; 4:37pm
URL: http://imagej.273.s1.nabble.com/Results-Table-in-Batch-Processing-tp5009182.html

Hello ImageJ Users,

I hope I have not missed something obvious, but here is my issue.  I have been using ImageJ to batch process approximately 5000 files at at time using Analyze Particles.  Even though the setBatchMode flag is set to true, the Results table displays to screen.  The code runs fairly fast at the beginning, but bogs down as more and more lines of results are added, which is understandable.  If I close the Results table while the script is running, it reopens and speeds up again.

I want to speed up the processing of these images, preferably so that I could submit the jobs to a cluster.  I tried it with Fiji yesterday in headless mode for the first time on my mac, and it worked for a while before it threw an exception.  I am not sure if it was a memory issue or something else.  I increased the allowed memory usage and it did make it further before dying.  Previously, I had been using IJ1 where the script worked fine (no memory issues), albeit slow as described.

It seems like my options are to either create a results file for each image file, which is tedious to post-process, or that I am missing something in the Analyze Particles call that would take care of this issue.  I know I have it set to display, but it seems like I cannot save the results table when I tell it not to display.

I am grateful for any advice.

For reference, here is the relevant part of the script, which is within a for-loop cycling over the files:
*****

getStatistics(area, mean, min, max);

setThreshold(10, max);

run("Set Measurements...", "area mean min centroid integrated limit redirect=None decimal=3");

run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00 show=Nothing display");


saveAs("Results", dir1+"Results.txt");

     close();

*****

Thank you,
Mary

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Mary F. Kidd
Assistant Professor, Physics Department

Tennessee Technological University
PO Box 5051
Cookeville, TN 38501

Office:  [phone]

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