Abstract:

Extracellular electrophysiology (ephys) is the most widely used technique to probe neural activity at single-neuron resolution at large scale. The recent development of high-density CMOS-based probes, such as Neuropixels, has further pushed the boundaries of this technique, enabling researchers to record thousands of neurons simultaneously.

Processing ephys poses several challenges for efficiency, standardization, and reproducibility. In this seminar, I will present several tools and projects designed to facilitate end users in utilizing community-developed state-of-the-art solutions for ephys data processing, storage, and sharing.

I will first introduce SpikeInterface, a powerful tool that includes a large variety of methods for all steps of the involved in the processing pipeline, including pre- and post-processing, spike sorting, automated and manual curation, visualization, comparison, and more.

Next, I will present an end-to-end processing pipeline (aind-ephys-pipeline), developed at the Allen Institute for Neural Dynamics which provides a reproducible, scalable, modular, and portable plug-and-play solution for processing large-scale ephys data.

To conclude, I will talk about community efforts for data storage and standardization as well as data sharing and re-use, specifically covering the Neurodata Without Borders (NWB) and DANDI archive projects.