SpikeForest documentation

SpikeForest is an open-source benchmarking website for spike sorting algorithms. The front end is under development here.

You can view these docs either on the hosted website or on the github repo.

Overview of the system -- in progress

Overview notebooks

Assembling the recordings and studies

The following notebook is used to assemble the recordings and studies that populate the website and to provide the input to the batch processing.

Batch processing

Processing is organized in batches that are stored on kbucket. An online notebook is used to assemble the batches. The batch processing can then be launched on any computer, for example a compute cluster. The scripts are written such that parallelization is achieved by running the same script simultaneously on many different cores / compute nodes. The pairio database is used to coordinate the jobs so that each script will perform different sorting jobs.

Exploring studies and processing results

The studies and sorting results of SpikeForest can be browsed/explored from any python notebook using the SpikeForest python API. An example of this is found in the below notebook.

The source code for this API is here (TODO: document this API).

Here's a notebook for plotting accuracy vs SNR for various algorithms:

Loading data from JavaScript

TODO: this section needs to be expanded to describe how to load spike sorting results

Meeting notes

More technical info

Old stuff

SpikeForest processing notebooks

Note: This section needs to be revised -- the pipeline has been overhauled -- docs are being assembled above