In summary, I am selecting circular ROIs containing Golgi-specific structures from transmission electron microscopy images. WITHIN these circular ROIs, I want to do manual segmentation (outline tracing) of Golgi structures. I have approximately 50 images with approximately 30-150 objects to segment in each. (I later want to sort and count these object into categories based on their morphology and e.g. distance to each other, but I will leave that out from this topic.)
I add an image to clarify a bit more what I am aiming at here: https://gubox.box.com/s/pf4z0ry8al1r2js8u6y1ez18w51gilil
I spent a lot of time trying to automate the segmentation, and I also tried Ilastik for that. I then concluded that this was probably one of these times where you just have to do the hard work, instead of looking for clever workarounds…
Now, what is constantly interrupting my process is this: As I segment the object inside the ROIs sometimes I would accidentally click in a way that will move the circular ROI, and then the segmentation I was making at that moment would be lost, and I would have to start over. This impacts the progression speed a lot. I would assume that there is a simple way to get around this.
Do you have any thoughts of how to improve the workflow and get rid of these constant interruptions? Can I burn the circular ROIs into the image in some way? Is there a better program for this than ImageJ? Is there something easier than the polygon tool? Any suggestions are welcome.
This post is doing something similar, but with a plugin I have no knowledge of. Also, the problem does not seem to be the sam. I include the link anyway: Select and measure multiple ROIs within the bigger ROI
This is my first post here, and I tried to follow all guidelines (but if you notice something, please tell me - I always have room for improvement).
Thanks a lot in advance!