How to record intensities for individual cells in time-lapse movie

Hello. I have recorded a movie (calcium imaging). From this movie I want to label individual cell (one at a time) and to build intensity plot for each time frame. How is it possible to do?

Pnevmatikakis et al. propose a complete Matlab pipeline for large scale calcium imaging data analysis in this paper:

You can find the Matlab source here:

Iā€™m not aware of a similar solution using ImageJ, but would be happy to see alternative approaches.

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