Event Date
ALESSIO BUCCINO, PHD
Electrophysiology Pipeline Engineer Consultant, Allen Institute for Neural Dynamics
Neurodata Scientist, CatalystNeuro
This is an in-person event. A registration link will be added soon.
Host: Roy Ben-Shalom, PhD, rbenshalom@health.ucdavis.edu
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 large-scale ephys data poses several challenges for efficiency, standardization, and reproducibility, given the increasing size and complexity of the datasets and the scattered ecosystem of analysis tools and software.
In this seminar, I will first focus on the community efforts to provide a unified and state-of-the-art toolkit to process ephys data. I will introduce SpikeInterface, a powerful tool that includes a large variety of methods for all steps 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. Finally, 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.
The second part of my talk will focus on the combination of high-density ephys data and computational modeling to develop and benchmark novel methods for data analysis, from spike sorting benchmarking to axon reconstruction.
Bio
Alessio Buccino, PhD is an engineer and software developer focused on methods and analysis tools for neuroscience research, especially for extracellular electrophysiology. He is passionate about science, software, and engineering, and his mission is to support neuroscientists and facilitate their research efforts by providing state-of-the-art analysis methods and software tools. Among these, he is the core developer of several open-source scientific tools, including SpikeInterface, a widely used software framework to unify and simplify the analysis of extracellular electrophysiology data.
Dr. Buccino joined the Allen Institute for Neural Dynamics team as an electrophysiology pipeline development engineer consultant in March 2022, with the goal of building open-source and computationally efficient processing pipelines to analyze large amounts of electrophysiological data. Since July 2020, he has been working part-time at CatalystNeuro, a consulting company with the mission of facilitating collaborations in neuroscience and standardizing data analysis and data storage solutions.
Alessio Buccino received his PhD from the Center for Integrated Neuroplasticity CINPLA, at the University of Oslo. He was a Postdoctoral Fellow at the Bio Engineering Lab at ETH, working on multimodal approaches to probe neural activity and to construct detailed biophysical models.