RE: batch processing macro problem.

Posted by jacob goodwin on Feb 24, 2015; 10:02am
URL: http://imagej.273.s1.nabble.com/batch-processing-macro-problem-tp5011621p5011749.html

Hi Christine,

Unfortunately no luck.  I was running the most recent version of imagej on both mac (os  x 10.8.5) and pc (windows 8), and also tried the other versions that were on the website.  I downloaded Fiji, both the continuous release and the Fiji life line November25th version for mac.   The continuous version didn't work, but the Nov 25th version did... almost.

So when I select process>batch>macro, I then put in the input and output folders, say that I want to save as a tiff, and the open up the macro that you wrote, then click ok.  It then asks me again for an input folder, and then for an ouput folder. It starts to process everything and then it asks me again for an input/output folder, if I let it it will continuously ask for this. The only way to stop it is to actually force quit the program.  The more I put in the input/ouput folders the more single images it now saves to my output folder.

I set up the input folder with 3 sets of images to process, if I look at the output folder after I first start it, there are 3 montages and one normal 488 image saved to the folder.  The first montage is correct, the second and third are mixed around.  The dapi image from A1, is placed as a 488 image in A2, and then the dapi image from A2 is placed in the 488 image for A3.

The PC version of Fiji doesn't even get that far, it makes the first montage and then only ever saves single images.