How to auto trace outline of ROIs


Hi, I am processing an image like attached, aiming to trace out all myelinated axon crosssections (loops with dark outline, exemplified as that yellow tracing) into ROIs for later morphometric analysis. As it is very tedious and time consuming to do it manually, I am wondering if there’s auto-detecting method available to facilitate this process. It doesn’t need to be fully automatic, as I can manually revise ROIs based on a reasonable auto-detection. Any suggestion/macros are appreciated. Thanks a lot

Hello @Xuefeng_Liu and welcome to the ImageJ forum!

Can you post your original image at good quality? Also, what segmentation methods have you tried already? It looks like the Trainable Weka Segmentation plugin could make a good job.

ignacio

Thank you. That was the quality of image that I have to work with. I was just using pure manual tracing but have just started to test Oufti. i will also look into the Weka plugin you suggested, seems to be a good method. i will keep you posted.