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alejoe91/README.md

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.

Twitter Mastodon

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

Pinned

  1. CINPLA/tracking-plugin CINPLA/tracking-plugin Public

    Open Ephys plugins for tracking experiments

    C++ 10 19

  2. SpikeInterface/MEArec SpikeInterface/MEArec Public

    Fast and customizable of extracellular recordings on MEA

    AGS Script 39 18

  3. MEAutility MEAutility Public

    Python package for multi-electrode array handling and stimulation

    Jupyter Notebook 10 4

  4. axon_velocity axon_velocity Public

    Python package to reconstruct axonal branches from high-density micro-electrode arrays

    Jupyter Notebook 1

  5. SpikeInterface/spikeinterface SpikeInterface/spikeinterface Public

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

    Python 402 151

  6. SpikeInterface/probeinterface SpikeInterface/probeinterface Public

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

    Python 37 33