Measuring the Intensities of Moving Cells

Hello, I am currently trying to perform cell segmentation on moving T-cells and to measure the intensities of these moving T-cells over time. Previously, I used FIJI’s Trainable Weka Segmentation plugin on a Z-max projection of my image stack to create a probability map. Then, I would use FIJI’s Threshold and Analyze Particles functions to create ROI’s that I could then simply overlay onto the original stack, which I would then measure via the ROI manager’s multi-measure command.

Unfortunately, these cells stayed still while I imaged them. With my new set of images, some of the cells float around a little, and so I can’t create a Z-max projection. I am having difficulty with creating ROI’s that can identify and move with a cell as it floats around and allows me to keep measuring the cell’s intensity across the stack.

I’m not using a macro, just using MATLAB’s built-in plugins and functions.

1 Like