I am working on some image analyses for my research that are based on colors found in specific parts of flowers. I used the program Ilastik to create segmentations from a large training set of image. As far as I can tell, Ilastik can only output black and white images from the resulting segmentation training.
Our pipeline currently looks like this:
The original image
the segmentation showing just the petals
the segmentation showing all the parts of the flower we want
Ultimately we just want the petals in one image and the anthers in another preferably as jpgs or pngs (like shown below) but these were created manually using the load selection tool, deleting the selection then saving the file. I tried recording those actions but was unable to get it to automate the selection of the masking file.