Code accompanying the paper "Fast Active Set Method for Online Spike Inference from Calcium Imaging". [arXiv, 2016]
Python: https://github.com/j-friedrich/OASIS
MATLAB: https://github.com/zhoupc/OASIS_matlab
The implementation of OASIS requires several functions for different formulation of the optimization problems. They can be found within the folder OASIS_matlab/oasis/. However, we highly recommend you use the wrapper function deconvolveCa.m to run differnet algorithms with one command.
| AR1 | AR2 | convolution ( difference of 2 expfunctions) | convolution | |
|---|---|---|---|---|
| FOOPSI[1] | √ | √ | √ | √ |
| Constrained-FOOPSI[2] | √ | |||
| Thresholded-FOOPSI[3] | √ | √ |
Run setup.m to add OASIS function to the search path of MATLAB
>> setup
The scripts to reproduce the figures are in the subfolder 'examples' with names obvious from the arXiv paper. They can be run with
>> run examples/paper/fig*.m
There is also a function deconvolveCa.m wrapping all formulations of the problem. You might only need this one for your problem. See a list of examples in the demo script oasis_test.m,
>> edit examples/all_examples.m
[1]Vogelstein, J.T., Packer, A.M., Machado, T.A., Sippy, T., Babadi, B., Yuste, R. and Paninski, L., 2010. Fast nonnegative deconvolution for spike train inference from population calcium imaging. Journal of neurophysiology,104(6), pp.3691-3704.
[2]Pnevmatikakis, E.A., Soudry, D., Gao, Y., Machado, T.A., Merel, J., Pfau, D., Reardon, T., Mu, Y., Lacefield, C., Yang, W. and Ahrens, M., 2016. Simultaneous denoising, deconvolution, and demixing of calcium imaging data. Neuron, 89(2), pp.285-299.
[3]Friedrich, J., Zhou, P., and Paninski, L., 2016. Fast Active Set Methods for Online Deconvolution of Calcium Imaging Data. *arXiv preprint arXiv:*1609.00639.