This is really cool! Have you tried using superpixel segmentation? It works well for some biological applications. Grabcut is also immensely useful.
We've been working on a platform for medical image and video annotation tasks. This means we need to support everything from DICOM to large pathology images, and endoscopy videos. We also have it connected to deep learning networks (e.g. Inception v3, YOLO, ENet) so you can easily train or download the JSON for offline analysis.
We'd love to have beta testers from the HN community: https://semantic.md/annotate.html