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Alessio Buccino

Hi everyone!

I am an engineer and software developer focused on methods and analysis tools for neuroscience research, especially for extracellular electrophysiology. I am passionate about science, software, and engineering, and my mission is to support neuroscientists and facilitate their research efforts by providing state-of-the-art analysis methods and software tools. Among these, I am 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.

In March 2022, I joined the Allen Institute for Neural Dynamics team as an electrophysiology pipeline development engineer consultant, with the goal of building open-source and computationally efficient processing pipelines to analyze large amounts of electrophysiological data. Since July 2020, I have 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.

Previously, I 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. Before that I was at the Center for Integrated Neuroplasticity CINPLA, at the University of Oslo, where I received my PhD.

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Software and Projects

  • SpikeInterface: unified and open-source Python framework for spike sorting. Features include loading/saving in several file format, pre-, post-processing, running 10+ different spike sorters, validation (quality metrics - QC), export to Phy, automatic curation based on QC, comparison between sorting outputs, and visualization widgets.

  • ProbeInterface: unified and open-source Python framework for handling neural probes.

  • MEArec: Python-based simulator of extracellular spiking activity for spike sorting development and validation. Features include: replication of bursting, control of spatio-temporal collisions, slow and fast drifts, several noise models. Fully interfaced with SpikeInterface.

Other resources

Alessio Buccino's Projects

numcodecs icon numcodecs

A Python package providing buffer compression and transformation codecs for use in data storage and communication applications.

nwb-jupyter-widgets icon nwb-jupyter-widgets

Explore the hierarchical structure of NWB 2.0 files and visualize data with Jupyter widgets.

orica icon orica

Online Recursive Independent Component Analysis

phy icon phy

phy: interactive visualization and manual spike sorting of large-scale ephys data

phylib icon phylib

Lightweight electrophysiological data analysis library

picard icon picard

Preconditioned ICA for Real Data

probeinterface icon probeinterface

Python package to handle probe layout, geometry and wiring to device.

pynwb icon pynwb

A Python API for working with Neurodata stored in the NWB Format

python-neo icon python-neo

Neo is a package for representing electrophysiology data in Python, together with support for reading a wide range of neurophysiology file formats

sphinx-jax icon sphinx-jax

Example how to use mathjax with sphinx -- the rendering is very slow

spikeinterface icon spikeinterface

A Python-based module for creating flexible and robust spike sorting pipelines.

spiketoolkit icon spiketoolkit

Python-based tools for running, curating, evaluating, and comparing popular spike sorting algorithms

spikewidgets icon spikewidgets

Python plots and widgets relevant to spike sorting and electrophysiology

staged-recipes icon staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

visual_analysis icon visual_analysis

This repository contains analytical functions used in my master project

wavpack icon wavpack

WavPack encode/decode library, command-line programs, and several plugins

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