Pestilli Lab

Projects

Platforms, consortia and programs

We started, direct, or run the data side of the national and international efforts below. All of them are open: the data, software, and frameworks they produce are meant to be used by anyone.

Founder & Director brainlife.io

brainlife.io

Open, free cloud platform for neuroscience · 6,000+ registered users · github.com/brainlife

brainlife.io connects neuroimaging data to versioned applications, parameters, and outputs in one place, and runs them on cloud systems and high-performance clusters. Every analysis is recorded as a provenance graph, so anyone can reproduce a result exactly, rerun it with a different model, or apply it to a new population. It handles MRI, diffusion MRI, MEG/EEG, and other modalities, and it is used for research and for teaching at institutions that have no computing of their own.

We started building brainlife.io in 2015. It is now the base for most of what the lab does: it hosts the data and processing services for the brain-connectivity consortia below, and its provenance model is where our work on AI-ready, agent-mediated science starts.

Principal Investigator brain-connects.org

BRAIN CONNECTS · Axonal Projectome Exchange (APEX)

NIH BRAIN Initiative Data Coordination Center · NINDS U24 · 2024–2029 · MPI: Anastasia Yendiki (MGH / Harvard) · Co-Is at the University of Minnesota and the Allen Institute

BRAIN CONNECTS is the NIH BRAIN Initiative program to develop the technology for mapping wiring across the whole brain, from single axons to long-range projections. APEX is the program’s data coordination center, which we develop and host. We build the data technologies, standards, and quality metrics for combining connectivity measurements from microscopy, tract tracing, and MRI across species, delivered through services such as connects.brainlife.io.

The systems have to handle petabyte-scale reconstruction while keeping track of how tissue samples, coordinates, reconstruction methods, and uncertainty relate to one another, so that the anatomy can support reproducible inference as the data grow. We also organize the consortium’s annual meetings and hackathons.

Director of Data Technologies mesoscale-connectivity.org

Center for Mesoscale Connectomics

NIH BRAIN CONNECTS UM1 · 2023–2028 · PI: Kamil Ugurbil (University of Minnesota) · a multimodal, cross-species approach

The Center for Mesoscale Connectomics images the same non-human primate brains with tract tracing, polarization-sensitive optical imaging, light-sheet microscopy, and ultra-high-field MRI, starting with the frontoparietal systems that support attention and cognitive control. The goal is a wiring map in which the same axons can be followed at every scale of measurement. That is the ground truth human tractography has been missing.

We lead the center’s data informatics: the standards, pipelines, and web services that bring multi-terabyte imaging volumes together with MRI, keep them registered to one another, and release them for anyone to use.

Principal Investigator bridge.incf.org

BRIDGE · Brain Research International Data Governance Exchange

Wellcome Trust · 2023–2027 · Co-Is: Damian Eke (Nottingham), Thomas Nichols (Oxford), Ricardo Chavarriaga (ZHAW Zurich), Amadi Ihunwo (Witwatersrand), Fernanda Tovar Moll (D’Or Institute) · powered by INCF

BRIDGE is building an international governance framework for brain and mental-health data. It brings together neuroscientists, lawyers, ethicists, regulators, and people with lived experience from Africa, Europe, and the Americas; has assessed the laws of more than ninety countries; and produces legal guides, technology, and a living handbook on international data governance, so that regulation does not stop research.

We have held regional and global workshops in Austin (2024) and Johannesburg (2025). The long-term goal is a self-sustaining global consortium that keeps the framework current.

Lead braindatagovernance.org

Global Brain Governance

An open ecosystem of tools for sharing brain data across borders · maintained by the lab · funded by Wellcome

Global Brain Governance turns the research from BRIDGE into tools that collaborations can use now: a legal map of how jurisdictions regulate neural data, kept up to date; decision tools that classify risk and choose a transfer pathway; a modular agreement for transferring and accessing neurodata; machine-readable governance labels; and a proposed registry of models trained on neural data. The aim is that protections stay in place as data move, are transformed, and are used to train AI.

Partners include the BRIDGE community, the University of Nottingham, ZHAW Zurich, the D’Or Institute, the University of the Witwatersrand, the University of Oxford, McGill University, and the International Brain Initiative.

Standards & community bids.neuroimaging.io

Data standards and community infrastructure

Brain Imaging Data Structure (BIDS) Steering Committee · INCF Infrastructure Committee chair · International Brain Initiative data-sharing working group

We led the BIDS Connectivity project, a community extension of the Brain Imaging Data Structure that describes macroscopic brain connections and the workflows that produce them, and we develop ezBIDS, a tool that walks people through converting raw scanner data into the standard so that it works with the major archives and platforms.

Franco Pestilli serves on the BIDS Steering Committee, chairs the Infrastructure Committee of the International Neuroinformatics Coordinating Facility (INCF), and chaired the data-sharing working group of the International Brain Initiative. Earlier infrastructure work includes the Advanced Computational Neuroscience Network and the connectome-mapping algorithms developed under the NSF BRAIN and Big Data programs.

Funding

Active and recent support

We are grateful to the agencies and foundations that make this work possible.

ProjectSourceYearsRole
BRAIN CONNECTS: The Axonal Projectome Exchange (APEX)NIH NINDS (BRAIN Initiative)2024–2029PI
Developing an international governance framework to advance global brain and mental health data equity and innovation (BRIDGE)Wellcome Trust2023–2027PI
Center for Mesoscale Connectomics: a multimodal, cross-species approachNIH BRAIN CONNECTS (UM1)2023–2028Co-PI
Extending ezBIDS, NiiVue and dcm2niix for user-friendly cloud-based integration and visualizationNIH NIMH (BRAIN Initiative)2023–2026Co-I
CRCNS: Dense sampling of brain function and structure to evaluate neural mechanisms of learning in early childhoodNational Science Foundation2023–2026Co-PI
Risk factors for the prospective development of alcohol use disorders in young adults with bipolar disorderNIH NIAAA2023–2028Co-I
A community-driven development of BIDS to describe macroscopic brain connectionsNIH NIMH (BRAIN Initiative)2021–2023PI
A pilot study to develop international data governance for neuroscienceThe Kavli Foundation2022–2024PI
Advancing science and education via human–AI cooperation on data, analyses, and publicationsMicrosoft Investigator Fellowship2020–PI
A personalized approach to predicting long-term neuropsychiatric outcomes in TBIU.S. Department of Defense2020–2024Co-PI
CRCNS US-France: lowering the barrier of entry to network neuroscience via open scienceNIH NIBIB2019–2023Co-PI
CRCNS US-German: DataLad — a decentralized system for digital objects of scienceNational Science Foundation2019–2023PI
NCS-FO: Connectome mapping algorithms with application to community services for big-data neuroscienceNSF (BRAIN Initiative)2017–2023PI
BD Spokes: Advanced Computational Neuroscience Network (ACNN)NSF (Big Data)2016–2022PI

Recognition

Awards, fellowships and honors

  • 2026Selected College of Liberal Arts candidate for the UT Austin President's Research Impact Award
  • 2023Honorary Distinction, Society of African Neuroscientists, Johannesburg
  • 2022Gift from The Kavli Foundation for international data governance in neuroscience
  • 2019Microsoft Investigator Fellowship (15 selected worldwide; the only awardee outside computer science and engineering)
  • 2017Fellow, Psychonomic Society
  • 2016Janet Taylor Spence Award for Transformative Early Career Contributions, Association for Psychological Science
  • 2016Fellow, Association for Psychological Science
  • 2016Indiana University nominee for the Blavatnik Award
  • 2011Postdoctoral Fellowship, Japan Society for the Promotion of Science (RIKEN)
  • 2009Fellow, Italian Academy for Advanced Studies, Columbia University
  • 2018–25Editorial boards of Scientific Data and Scientific Reports (Springer Nature); acting editor, PNAS
  • 2025–Steering Committee, Brain Imaging Data Structure (BIDS)