Good day Avi Jacob,
no doubt TransformJ is an excellent piece of software but perhaps
ImageJ's "Transform > Translate" will do the job.
If you must shift your images for an integer amount of pixels (you write
seven) the recorded macro call is:
run("Translate...", "x=0 y=7 interpolation=None");
There are many IJ-macro examples that show you how to batch process all
images in a folder. However, you may also have a look at the IJ-batch
processing item under menu "Process > Batch > etc.". For details please
consult the various IJ-documentations.
HTH
Herbie
:::::::::::::::::::::::::::::::::::
On 15.12.13 10:32, Avi Jacob wrote:
> 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/>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
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