Image Annotation Tools

I want to mark the cell boundaries in images like below. [Then I plan to use it for benchmarking and maybe for trying out a few semi-supervised ML-based approach]. I basically want to generate a mask of the cell membrane. I’m able to generate some pre-final mask for images, which approximately label 80% of the cell membrane and I would like to use them to make the annotation process faster.

I’ve tried using RatSnake (But it is designed to be used for closed shape selection like a polygon). And most annotation tools, that I found, were a retangular selection based. Any tips on how can I label such images? Maybe in Photoshop or ImageJ?

I’m a noob in this area and any literature or media on this topic would be helpful.

Thanks :smiley:

Hello Siddharth,

First of all, is this the raw image? Do you have a version of higher quality?

There is probably no need for you to do manual annotation, simple thresholding steps should give you a pretty good selection of membranes.

This is what I got from your very blurry image, with just a couple of steps.

If you do want to manually annotate the images, ImageJ has many options for this, simply select a tool from the toolbar.

Best,

Sverre