Overview

GOAL As stated on the homepage, "The goal is to have this repo as your one-stop-shop for code you may need as a Buzsaki Lab member."

APPROACH We have chosen to use a mostly matlab-based approach and hope make a collection of functions for analysis of electrophysiologic, behavioral and other aspects of data from our neuroscience experiments.

We break our repository into preprocessing elements (automated processing to extract LFP and spiking activity which are the basis of nearly all of our work) and analysis elements that will be individualized to the particular experiment and experimenter.

We have also created standardized data storage formats to interact with this standardized code.

PREPROCESSING We have not yet agreed on a single preprocessing stream and we may not ever. However we have agreed that regardless of the preprocessing stream we will converge all preprocessing results into a single set of formats that can then be used by our analysis code. Those formats are described under the Data Formatting Standards page on the wiki.

ANALYSIS SCRIPTS We have chosen, after a great deal of consideration, to base many of our functions on the FMAToolbox (available as a sub-package here: https://github.com/buzsakilab/buzcode/tree/master/externalPackages/FMAToolbox). For maintenance of backwards compatibility with pre-existing scripts we have opted to leave these scripts untouched and with the same function names.

We have then copied and modified many of those scripts into our own functions with names starting "bz_". For instance bz_FindRipples.m is based on FindRipples.m from the original FMA toolbox and both can be found in this repository. The bz_ label for all functions we create and/or modify That way we avoid name duplication with the other external packages (and all our code can be searched in matlab with TAB autocomplete).

DATA FORMATS Along with standardized scripts we will have standardized data formats. These data formats are designed to be transparent and to have a "proper" level of modularity/complexity - allowing one to save relevant extracted aspects of data without having to reprocess them, but without too much clutter.

Additionally it is worth noting that a major expectation is that

1. Separate recordings are stored separately in independent folders (with foldernames matching recording names?)

2. Files relating to each recording will be stored in the same folder as that recording.

   See our Data Formatting Standards page for more details

USE It is expected that code will be downloaded and maintained via git. See the wiki main page for links to more details, including how to download, how to contribute and code standards of practice for this repo.

See here for some ideas about how to use git https://gun.io/blog/how-to-github-fork-branch-and-pull-request/