jovo / smc-oopsi

code to implement our sequential monte carlo (smc) algorithm to perform optimal optical spike inference (oopsi) for individual neurons

This is a repository containing the code to implement the algorithms employed in Vogelstein et al, 2009, and subsequent related advances.
Publication version of manuscript is now available from [Cell Press] 4 with subscription, or [here] 5 for free.

Note that the code in this repository is not kept up-to-date; rather, it is an archive of our work.
for an up-to-date code base, check out: https://github.com/jovo/oopsi

This work may be cited as:

Vogelstein, Joshua T.; Watson, Brendon O.; Packer, Adam M.; Yuste, Rafael; Jedynak, Bruno; Paninski, Liam. Spike Inference from Calcium Imaging Using Sequential Monte Carlo Methods. Biophysical Journal, Volume 97, Issue 2, pp.636 - 655, 2009.

Repository Organization

• code: contains current stable version of code
• manuscript: contains everything related to [Vogelstein et al. 2009] 5, including ** code: version of code used for manuscript ** data: both raw data and data generated by simulations for figs ** figs: pdf's of figs in manuscript ** reviews&proofs: reviews and proofs from BJ to get this paper published ** tex: contains tex and compiled other files of submitted manuscript (and some minor revisions)
• general_background: a document containing some general background information that might be useful

Quick Tips

• final version of proof may be found [here] 1
• to learn how to use the algorithm, i suggest playing with scripts in the [script folder] 3
• any questions or issues, please use the [issues tab] 2
• any problems with that, or questions inappropriate for that forum, please contact me at: [email protected]
• please respect our policy of openness, and operate accordingly.

License

License stuff (apparently, this is useful for some people): Copyright (c) 2008 Joshua Vogelstein

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.