Cell Segmentation - Separating cells right next to each other

Hi all,

I'm new to MatLab, and I'm trying to write a cell segmentation program. I can detect single cells pretty easily by creating a binary mask and tracing the outline, but when two cells are next to each other, their binary masks combine together to form one blob. I'm trying to think of a way to separate the two (or more) cells that form the blob. I was thinking of maybe using a line to separate them and using the separated boundary to create an ROI, but this would only work for blobs made up of two cells, not a string of connected cells. I'm also thinking of having the user specify the center of the cell visually, find the closest distance to the edge of the binary mask from that center, and then create an ellipse.

Do the two ideas above sound feasible? Are there any other ideas?

This is my first question here, so forgive me if it's not in the right format or anything. I'll be up for clarifying anything!

Thank you so much!

Answer 1

[Image Analyst]

See Steve's demo:

http://blogs.mathworks.com/steve/2006/06/02/cell-segmentation/

[Tanya]

I tried implementing this method, but it doesn't detect the right cells at all.

[Image Analyst]

Then you need to keep working on it and adapting it until it works correctly. Do you know how many times the first time I try something it doesn't work? Usually. But I keep tweaking and improving until it works. I'm confident the same process will work for you.

[Peyman Obeidy]

There are some codes out there that you can use like (CellSegm-a MATLAB toolbox for high-throughput 3D cell segmentation.). But, I also like to be able to do that in my code.

[Peyman Obeidy]

one approach is to get help from your nuclei channel, use this to find the center and then the edge will be like the edge of a volcano if your standing in the middle of the volcano. but how do i do this :)