Re: Batch cropping a stack of visually overlaid images?

Posted by dscho on May 03, 2013; 3:51pm
URL: http://imagej.273.s1.nabble.com/Batch-cropping-a-stack-of-visually-overlaid-images-tp5002903p5002909.html

Hi Miles,

On Thu, 2 May 2013, Miles Wolbe wrote:

> Is it possible to visually overlay images in a stack and batch crop them
> like Briss does for PDFs?
>
> http://sourceforge.net/projects/briss/
>
> I tried Image > Stacks > Images to Stack, but only one image is visible
> on the stack instead of being overlaid.

You can make a z-projection of the stack, select a rectangular region of
interest, then close the projection, select the stack,
Edit>Selection>Restore Selection, and then crop.

You'll find it very easy to convert this into a macro (adding a
waitForUser when the z projection is shown to let the user specify the ROI
before going on) using the macro recorder.

Ciao,
Johannes

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