Batch cropping a stack of visually overlaid images?

[Miles Wolbe]

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.

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[dscho]

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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[Miles Wolbe]

Thanks so much, Johannes! That is exactly what I was after.

I have posted a walkthru for new users like me here:

http://tinyapps.org/blog/misc/201305030700_crop_images_like_briss.html

Aloha,

Miles

On May 3, 2013, at 05:51 , Johannes Schindelin wrote:

> 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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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Antoinette]

Batch image cropping can be the fastest way to handle multiple image cropping. And generally speaking, such batch image cropping tool can be used to crop common image file formats, like png, jpeg, gif, bmp and tiff. And we can specify the name and storage path of cropped image file.