Open Neuroimaging Laboratory

Open Neuroimaging Laboratory
Name	Open Neuroimaging Laboratory
Established	2017
Location	New York City
Director	PIs at multiple institutions
Fields	Neuroimaging, Cognitive Neuroscience, Computational Neuroscience

Open Neuroimaging Laboratory is a collaborative research initiative that promotes transparent, reproducible, and accessible neuroimaging science through open data, open software, and community-driven standards. The Laboratory operates across multiple academic centers and non-profit platforms to integrate tools, datasets, and practices used in functional magnetic resonance imaging, diffusion MRI, and electrophysiology. Its activities intersect with major initiatives and organizations in neuroscience and open science.

Overview

The Laboratory coordinates contributions from researchers affiliated with institutions such as Columbia University, Harvard University, Massachusetts Institute of Technology, University of California, Berkeley, Stanford University, University College London, University of Oxford, University of Cambridge, University of Pennsylvania, Yale University, New York University, Princeton University, and Johns Hopkins University while engaging platforms including OpenNeuro, NeuroVault, GitHub, Zenodo, OSF, and DataLad. Its remit spans interactions with funding agencies and consortia like the National Institutes of Health, Wellcome Trust, European Research Council, Human Connectome Project, Brain Initiative, Allen Institute for Brain Science, and NIH BRAIN. Leadership and contributors include investigators with backgrounds in labs associated with Michael Milham, Russell Poldrack, Tal Yarkoni, Sergei Gepshtein, Stephen Smith, Karl Friston, Joshua Tenenbaum, Tomaso Poggio, Anna Schapiro and others drawn from centers such as McGovern Institute for Brain Research and Center for Neuroscience and Society.

History and Development

The Laboratory emerged amid converging efforts exemplified by projects like the Human Connectome Project, UK Biobank, ADNI, OpenfMRI, BrainMap, and initiatives associated with Neuroinformatics. Early milestones involved harmonizing practices referenced in guidelines from Committee on Best Practices in Data Analysis and Sharing (COBIDAS), dialogues at conferences including Society for Neuroscience, Organization for Human Brain Mapping, Cognitive Neuroscience Society, and workshops sponsored by F1000Research and Nature Neuroscience. Founding contributors had ties to laboratories at Massachusetts General Hospital, Beth Israel Deaconess Medical Center, McGill University, Karolinska Institutet, Max Planck Society, and Riken. Technical development leveraged software from projects like FSL, AFNI, SPM, FreeSurfer, Nipype, BIDS, and fMRIPrep, with policy influence from institutions such as Open Science Framework and journals like Nature, Science, Neuron, and PLOS Biology.

Research Focus and Methods

Research spans multimodal neuroimaging combining methods rooted in tools like fMRIPrep, dMRI, resting-state fMRI, task-based fMRI, electroencephalography, and magnetoencephalography with analytic frameworks using Bayesian statistics, machine learning, deep learning, multivariate pattern analysis, and connectomics. Methodological advances draw on algorithms and libraries from scikit-learn, TensorFlow, PyTorch, NumPy, and MATLAB toolboxes used in labs at Carnegie Mellon University, University of Washington, Dartmouth College, University of Toronto, Brown University, and University of Michigan. Validation and reproducibility activities reference benchmark datasets produced by OpenNeuro, UK Biobank, Human Connectome Project, ADNI, ABIDE, CamCAN, and NKI-Rockland Sample while adhering to metadata standards developed by BIDS and provenance systems influenced by PROV.

Open Science Practices and Resources

The Laboratory advocates for open data sharing, open-source software, open workflows, and transparent reporting consistent with policies from NIH, Wellcome Trust, European Commission, and publishers including PLOS, eLife, Nature Communications, and Science Advances. It curates and contributes to repositories and tools such as OpenNeuro, NeuroVault, Neurodata Without Borders, DataLad, BIDS, fMRIPrep, MRIQC, Docker (software), and Singularity (software), and promotes licensing practices like Creative Commons and MIT License. Training and dissemination occur via workshops at venues like Organization for Human Brain Mapping, Society for Neuroscience, Neuroinformatics, summer schools at Wellcome Trust Centre for Neuroimaging, and online resources hosted on GitHub and Zenodo.

Collaborations and Community Engagement

Community engagement includes partnerships with consortia and institutions such as Human Connectome Project, Allen Institute for Brain Science, UK Biobank, ADNI, OpenfMRI, ABIDE, NKI-Rockland Sample, INCF, EBRAINS, European Molecular Biology Laboratory, National Institutes of Health, and professional societies like Organization for Human Brain Mapping and Society for Neuroscience. The Laboratory organizes hackathons and training programs in collaboration with research groups at Harvard Medical School, Massachusetts Institute of Technology, Stanford University, University of Oxford, University College London, Princeton University, Yale University, and community platforms including Mozilla Science Lab and ReproducibiliTea.

Impact and Key Projects

Key projects include creation and curation of open neuroimaging datasets, development of reproducible pipelines (e.g., integrations with fMRIPrep, Nipype, BIDS), tooling for data provenance with DataLad and Datalad, quality control tools like MRIQC, and collaborative publications with teams at Harvard University, Stanford University, Massachusetts Institute of Technology, Columbia University, University of California, Los Angeles, Johns Hopkins University, University of Pennsylvania, Princeton University, University College London, and University of Oxford. Impact is reflected in citations within journals such as Nature Neuroscience, Neuron, PLOS Biology, eLife, Scientific Reports, and influence on policy from NIH, Wellcome Trust, and European Research Council. The Laboratory’s outputs have enabled secondary analyses by researchers at University of California, Berkeley, McGill University, Karolinska Institutet, Max Planck Society, Riken, University of Toronto, University of Michigan, University of Washington, Dartmouth College, and Brown University.

Category:Neuroscience research organizations