Using the "crop and keep ROI" script for images with multiple ROIs

[Michael Delves]

Hi,

I have images with multiple ROIs (different cells). I would like to crop all the individual cells into their own files but overlay and keep their original individual ROIs. I came across the "crop and keep ROI" script (http://icy.bioimageanalysis.org/script/Crop_and_keep_ROI) that perfectly does this for one ROI and you can manually instruct it which ROI to operate on. Sorry my programming skills are very basic. Is there a way to loop this process through all the ROIs in the image - even better if it can be integrated into Protocols.

Thanks!

[Stephane]

Hi Michael,

You have a ready to use protocol for that :

http://icy.bioimageanalysis.org/protocol/Crop_sequence_to_ROI

I think it does exactly what you want :)

Best,

- Stephane

[Michael Delves]

Hi Stephane,

I've been using Crop_sequence_to_ROI but I have irregular polygon ROIs and it only crops to a rectangular bounding box surrounding the polygon ROI. I'd like to crop using Crop_sequence_to_ROI and then paste the original polygon ROI in place in the cropped image.

Outside of protocols you can do this by copying an ROIs and pasting it into a manually cropped image, then reposition it to pixel 0,0. I can't seem to replicate this functionality in protocols so I can iterate it over 100s of images with multiple ROIs.

Any ideas?

Thanks!!