Posted by
Christine Labno-2 on
URL: http://imagej.273.s1.nabble.com/batch-processing-macro-problem-tp5011621p5011756.html
Hi Jacob,
Sorry for the confusion. Don't use Process -> Batch Macro with the new version of the macro. Just open the macro and then from the Macro window choose Macro -> Run Macro. It's meant to stand alone, not work through the Batch. You will only be able to process one folder at a time, not a folder with a bunch of subfolders. See if that works. If that doesn't work I don't know what to do for you, not being able to see what's going on on your machine.
Best,
Christine
--------------------------------------------
Christine Labno, Ph.D.
Asst. Technical Director
Light Microscopy Core
University of Chicago
Office of Shared Research Facilities
KCBD 1250 900 E. 57th St.
(773) 834-9040 (phone)
________________________________________
From: ImageJ Interest Group [
[hidden email]] on behalf of jacob goodwin [
[hidden email]]
Sent: Tuesday, February 24, 2015 4:02 AM
To:
[hidden email]
Subject: Re: batch processing macro problem.
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.
A1--W00001--P00001--Z00000--T00000-- montage.jpg (434K) <
http://imagej.1557.x6.nabble.com/attachment/5011749/0/A1--W00001--P00001--Z00000--T00000--%20montage.jpg>
A1--W00001--P00001--Z00000--T00000--D montage.jpg (252K) <
http://imagej.1557.x6.nabble.com/attachment/5011749/1/A1--W00001--P00001--Z00000--T00000--D%20montage.jpg>
A1--W00001--P00002--Z00000--T00000--D montage.jpg (274K) <
http://imagej.1557.x6.nabble.com/attachment/5011749/2/A1--W00001--P00002--Z00000--T00000--D%20montage.jpg>
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