Auto Cropping

[SeanCullen11]

I'm looking to use the auto crop function of plantcv to help crop an image containing several leaves into an image of each leaf. I have a large data set of leaves to crop so this would be extremely helpful. Looking at the documentation I'm confused what object is meant to be passed into the obj argument of the auto_crop function. It seems to ask for a contour but the documentation isn't clear on how to make those.
Any help would be greatly appreciated

[HaleySchuhl]

Hi @SeanCullen11 , thanks for reaching out! The pcv.find_objects function will return a list of contours from a binary mask. Another method that might be a better approach depending on your images would be to use pcv.roi.multi and then pcv.roi_objects to filter down the contours within a binary mask so they can each get autocropped (example here.

[SeanCullen11]

Awesome, thank you! It seems like that would help as the images I am using all look like this. So you're suggesting to use the roi.multi and the roi_objects to get the contours then put those into the autocrop function to crop my image?

[HaleySchuhl]

Yup! The second documentation page that I linked includes a "next steps" section that has a for loop. You should be able to modify this example to do an auto_crop step for each leaf and then print out the individual leaf images to a file. This would also be the format for analyzing shape or any other traits per leaf.

Please let us know if any other questions come up!

[SeanCullen11]

Fantastic! Thank you for your help.