Our Portfolio

NWB expert and community outreach, DANDI project, MIT

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DANDI is a BRAIN-funded project to build an archive for publicly sharing cellular neurophysiology data collected by the BRAIN Initiative. My role in the project is to build support for NWB files, and to help the DANDI team reach out to NWB users to build a library of data.

NWB:N Community Liaison, Lawrence Berkeley National Laboratory sponsored by Kavli Foundation

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I help the systems neuroscience community adopt NWB:N 2.0 through triaging issues, core development, and community engagement like organizing hackathons and writing the newsletter. This contract funds consulting for labs to help with NWB:N 2.0 adoption. Until February 1, 2020 I am able to provide the following services free of charge:

  • Discuss how NWB adoption could accelerate scientific discovery in your lab and help determine if NWB is appropriate for you.
  • Help to create a project plan for NWB adoption into your labs ecosystem. I can help determine what analysis and conversion tools and extensions would be relevant for you.
  • Review pre-released NWB files for compliance with the NWB schema and best practices.

Lead Data Scientist of Ripple U19, Stanford University

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I am the lead data scientist for a collaboration between Ivan Soltesz (lead PI), Gyorgy Buzsaki, Atilla Losonczy, and Mark Schnitzer to elucidate the cellular mechanisms of hippocampal sharp wave ripples using calcium imaging, electrophysiology and large scale simulation.

My role is to help these groups collaborate, sharing data and analyses through the NWB:N 2.0 standard, and promote standardization in the broader neuroscience community.

I worked with the large scale simulation teams across several groups to establish a standard for simulation output as an NWB extension, and a converter from the SONATA format to NWB:N 2.0. With the help of Konstantinos Nasiotis, we built an NWB:N 2.0 reader in Brainstorm and worked with buzcode to read NWB:N 2.0 files. We have also released data collected by the Buzsaki Lab in NWB:N 2.0.

Simons Foundation NWB:N Adoption Pilot

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This pilot project with the Simons Foundation is aimed at helping labs adopt NWB:N while building and publicly releasing tools that will help other labs with the transition.

This initial pilot includes hippocampal recordings in NHPs from Beth Buffalo’s lab, neuropixel recordings from Lisa Giocomo’s lab, and volumetric calcium imaging of a fruit fly from Richard Axel’s lab.

Through this project we have been working with the CaImAn development team to support reading and writing NWB:N 2.0 files.

Lead of data engineering speech neuroscience collaboration, UCSF

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I am working with the labs of Dr. Edward Chang, Dr. Nitin Tandon, and Dr. Mark Richardson to use NWB:N 2.0 as a foundation for standardizing ECoG data. Through this effort we have restructured internal tools to work with the NWB:N format, and have publicly released high density ECoG recordings during speech. Through this project we built the NWB:N extension for storing the cortical surface of a subject. We enhanced the ECoG visualization library img_pipe to read NWB:N 2.0 files with this extension, and we created ecogVIS, a python GUI for visualizing and annotation of raw voltage traces and standard Chang Lab ECoG preprocessing.

* The institutions listed (Lawrence Berkeley National Labs, Stanford University and UCSF) are institutions with which I have a contract. I am not an employee of any of these institutions.

Availability for helping other labs

We are always interested in opportunities to I also manage a team of computational neuroscientists who help labs and teams of labs in more involved projects such as building conversion scripts, porting tools to NWB, and helping to package and publicly release data. If you are interested in working with us.

Our work is entirely open source. See GitHub repo for code of past and ongoing projects.