I am working on a class project where I am attempting to perform segmentation on images of copepods. The ultimate goal is to measure the prosome (body) length, excluding the tail segments.
I am still pretty new to image processing in general, so I am reaching out to the community to find out if anyone has other suggestions for tools I could try before I commit more time to training in ilastik.
Things I’ve tried:
I’ve trained in ilastik on pixel classification mode. It was underestimating the size of my copepods due to uncertainty on the edges. When I upped the level of precision in my annotations, the overall improvement in the results was very minimal.
I’ve also tried the findContours and fitEllipse functions in the python cv2 package. However, this is not currently finding the right contours or fitting ellipses to the correct place on the majority of images.
I am attaching several example photos.The grid segments are each 1 mm.
Thank you for any suggestions.