These are chat archives for epnev/ca_source_extraction
Matlab implementation of a source extraction and spike inference algorithm for large scale calcium imaging data analysis, based on a constrained matrix factorization approach.
Hi @Quantum_Neuron_twitter (sorry for the late response, make sure you tag me next time so I can get a message)
We have two algorithms that can operate directly on fluorescence traces.
1) A convex optimization approach that is used by the function
constrained_foopsi.m and you can use directly.
2) A Bayesian approach that is implemented in a different repo here
For option 1 a faster implementation can be found through OASIS, which is included in the package but also has its own repo.
constrained_foopsiso in essence they are equivalent. However there are a few heuristics implemented for hyperparameter estimation, plus it operates in a nearly online mode so it can be much faster especially for the AR1 case.