Crop according to pre-made outline

I was wondering if anyone knows a way to cut out the section of the uploaded image that is outlined in red (zooming in you can see better the pre-made outline) in order to obtain a new one with the highlighted structure only!

Ideally I would have to find a solution similar to this but unfortunately our outline is pre-made…

Hi @tweagles1,

I am not sure if I get it correctly what you try to achieve but here is a solution for the problem as I understand it.
if you want to keep the original over all size of the image and just show the marked region on a black background you can set the background color to black ►Edit►Options►Colors… and then click on ►Edit►Clear Outside. This sets all pixels outside your selection to black.
This assumes that your “outline” is existing as a ROI in ImageJ e.g. in the ROI Manager

If you want to get a new image with only the indicated part best is to duplicate it ►Image►Duplicate…
and thereafter you clear the outside as described before.

Good day,

is this

what you want?

Do you need to do this automatically?



Good day to you! Yes, this is exactly what I am looking for, hoping to automate the process! … how is it done?

My bad, I was overexcited by the speed of the reply and overlooked the part of the message below the image… automatically would be awesome, but I would have the red outline located in a different region according to the image, though. The one linked above is a sample one

Could you please confirm if the manual method works for you?


Yes indeed, manual selection and macro work perfectly for this image

Truly amazing, many thanks!