I would like to score tissue phenotypes in an image in a semi-automatic format. I tried using morphologic analysis to detect different shapes, but it hasn’t been really successful, so I think I’m just going to do it manually.
I have modified a macro on here to split my tif into 50 smaller rectangles (e.g. image1-tile001, image4-tile048, etc.). Now I have a folder containing the files I need. I would like to be able to:
- select a random image without repeat
- display that image on screen
- press a key to assign phenotype (e.g. 1=thick, 2=mixed, 3=sparse, 4=nucleus, 5=n/a)
- record the score with the image label
- move to next image
- at end of folder, show report with each image and percent of tiles for each image (e.g. “image 1: 20% class 1, 20% class 2, 10% class 3, 50% class 4, 3 tiles not scored”)
I’m thinking the best way to do this is probably with python or some macro within fiji. It makes me think of Anki flashcards I used back in med school. Am I asking in the right place?
Thanks in advance for your help!