How to batch TransformJ Translate in order to Y shift a channel?

Posted by Avi Jacob on Dec 15, 2013; 9:32am
URL: http://imagej.273.s1.nabble.com/How-to-batch-TransformJ-Translate-in-order-to-Y-shift-a-channel-tp5005915.html

Hello,

One of my 16bit channels is Y shifted (chromatic aberration or maybe some
other misalignment) as compared to the other, which throws off a
segmentation analysis. The TransformJ Transform plugin solves this problem
by allowing me to shift one channel by the 7 pixels it is shifted by.
However, I need to do this on 700 images at a time.
I cannot figure out a way to batch and perform this on all images in a
folder, automatically.

1. Is there another way to do the alignment?
I looked at the register plugins also, but as all I need is a simple Y
shift of n pixels, the TransformJ seems perfect. However, this seems to
work only on a single, open image. Optimally, I would like to run this on
all images in a folder and save them as new images, or even overwrite the
original images.

2. Seems to me that a macro might do the trick, but I am a novice at
writing macros.

Best,
Avi

--
Avi Jacob, Ph.D.
Research Associate
Bar-Ilan University, Ramat-Gan 5290002, Israel
http://lifefaculty.biu.ac.il/shav-tal/

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