search

AllenInstitute / ecephys_spike_sorting

Modules for processing extracellular electrophysiology data from Neuropixels probes
Other
109 stars 91 forks source link

Potential synergy between this repository and SpikeInterface #40

Closed colehurwitz closed 5 years ago

colehurwitz commented 5 years ago

Hello!

I am a developer working on an open-source suite of tools (SpikeInterface) designed to standardize extracellular analysis and spike sorting.

A lot of our work in the past year has gone into standardizing IO for both raw and sorted extracellular file formats, wrapping popular spike sorting algorithms in our framework, and developing comprehensive tools for ground truth analysis of different sorters (along with implementation of some preprocessing and postprocessing tools for spike sorting analysis).

One part of our framework that still needs a lot of work is in the unsupervised metrics that can be used to evaluate the result of a spike sorter on datasets without ground truth. Recently, we discovered this repository and were impressed by the large suite of implemented metrics for this express purpose. We would love to get in touch and even discuss over email/skype about a possible integration of these metrics into SpikeInterface.

If you want to get in touch over email, my email is cole.hurwitz@ed.ac.uk.

Best,

Cole Hurwitz

jsiegle commented 5 years ago

Hi Cole, I just looked through the SpikeInterface code and docs, I'm very glad this project exists! We'd be happy to help integrate our quality metrics code into your repository. It looks like they'd be going into this file?

In general, it would be helpful to get some feedback on what we've implemented so far, and to hopefully reach a consensus on exactly how these metrics should be computed. We've found that things like the method for sub-sampling spikes or the number of PCs included in the calculations can have a big impact on the results.

I'll send you an email to coordinate further!

colehurwitz commented 5 years ago

Hi Josh, thanks for getting back to me! I am glad that you are interested in our project!

You are correct, we would be integrating your metrics into the quality metrics file. Part of the challenge will be making your metrics compatible with our RecordingExtractors and SortingExtractors which standardize data retrieval from any raw and sorted file formats, respectively. We can discuss that in future correspondence.

We would also be excited to discuss the metrics you implemented so far. Jeremy Magland is one of the core developers of our framework and he has done some work on validating spike sorting algorithms without ground-truth information.

It would be great if you CC these people as well in your upcoming email. They are the main team (along with me) behind building this framework:

Jeremy Magland: jmagland@flatironinstitute.org Matthias Hennig: m.hennig@ed.ac.uk Alessio Buccino: alessiob@ifi.uio.no Samuel Garcia: samuel.garcia@cnrs.fr

jsiegle commented 5 years ago

These metrics have now been added to the SpikeMetrics repository.