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https://prismclinical.com/

Provides Prism softwares and services that integrate advanced imaging into the clinical workflow for brain mapping from acquisition through processing, visualization, and export to PACS. Prism integrates functional MRI, diffusion MRI, perfusion, MR spectroscopy, and PET/CT into a unified workflow for diagnosis and treatment planning in brain disorders. Processing is also available as a cloud deployed service, Prism Serve. Research support includes import/export for imaging and derived quantitative data in both DICOM and research formats such as AFNI and Trackviz.

Proper citation: Prism Clinical Imaging (RRID:SCR_016977) Copy   

•   Source: SciCrunch Registry

https://biccn.org/data

Searchable table of datasets. Data generated from projects through BRAIN Initiative Cell Census Network. Datasets can be filtered by species, research investigator, grant number or experimental technique. Includes links to data directories at data archives and links to protocols.

Proper citation: BICCN Cell Registry (RRID:SCR_017267) Copy   

•   Source: SciCrunch Registry

https://github.com/cwatson/braingraph/

Software R package for performing graph theory analyses of brain MRI data.

Proper citation: brainGraph (RRID:SCR_017260) Copy   

•   Source: SciCrunch Registry

http://www.brainimagelibrary.org

Public, NIH-funded repository and analysis ecosystem for brain microscopy data, designed to store, share, and process massive volumetric datasets. It enables researchers to access whole-brain images, neuron morphologies, and spatial data without needing to download, fostering collaborative discovery. Used to deposit, analyze, mine, share and interact with large brain image datasets.

Proper citation: Brain Image Library (RRID:SCR_017272) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/neuroinfo

Software for automatic identification and delineation of brain regions within experimental mouse brain sections. NeuroInfo registers serial section images of any orientation to Allen Mouse Brain Atlas, corrects for distortion due to histological processing, delineates anatomies in experimental section, and detects and reports on cell number within selected anatomies.

Proper citation: NeuroInfo (RRID:SCR_017346) Copy   

•   Source: SciCrunch Registry

https://github.com/zuoxinian/CCS

Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies.

Proper citation: Connectome Computation System (RRID:SCR_017342) Copy   

•   Source: SciCrunch Registry

https://github.com/Mark-Kramer/Seizure-Waves

Analysis and modeling code for waves of seizure activity.

Proper citation: Seizure-Waves (RRID:SCR_017455) Copy   

•   Source: SciCrunch Registry

https://brainreader.net

Developer of medical software to offer image analysis technologies. Company in Denmark that provides medical image processing software to get quantifiable and accurate insight into brain.

Proper citation: Brainreader (RRID:SCR_017308) Copy   

•   Source: SciCrunch Registry

https://www.ibis-network.org/index.html

Research study of brain development in infants and children with autism. Consortium of researchers across North America that work together to discover early changes in brain development of young children with autism. Participants will travel to their closest study location to receive developmental and behavioral assessments, MRI scan of the brain. Participants will be reimbursed for travel and related expenses. Families of children at high risk for developing symptoms of autism will receive assistance with referrals for local services. check if data repository is in the papers

Proper citation: IBIS Network (RRID:SCR_017399) Copy   

•   Source: SciCrunch Registry

https://kg.ebrains.eu/

Metadata management system built for EBRAINS. Multi modal metadata store which brings together information from different areas of Human Brain Project as well as from external partners. Graph database tracks linkage between experimental data and neuroscientific data science supporting more extensive data reuse and complex computational research.Supports rich terminologies, ontologies and controlled vocabularies. Built by design to support iterative elaborations of common standards and supports these by probabilistic suggestion and review systems.

Proper citation: EBRAINS Knowledge Graph (RRID:SCR_017612) Copy   

•   Source: SciCrunch Registry

https://www.leicabiosystems.com/histology-equipment/cryostats/leica-cm1520/

Cryostat for routine histology and cryosectioning including critical applications such as Mohs surgery. Brain sectioning. Actively cooled quick freezing shelf with defrost function and refrigeration system are provided.

Proper citation: Leica: CM1520 Cryostat (RRID:SCR_017543) Copy   

•   Source: SciCrunch Registry

http://www.iu.edu/~beca/

Visualization and analysis software for interactive visual exploration and mining of fiber-tracts and brain networks with their genetic determinants and functional outcomes. BECA includes an fMRI and Diseases Analysis version as well as a Genome Explorer version.

Proper citation: BECA (RRID:SCR_015846) Copy   

•   Source: SciCrunch Registry

https://biccn.org

Consortium for the cell census in the brain. Integrated network of data generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate brains.

Proper citation: BICCN (RRID:SCR_015820) Copy   

•   Source: SciCrunch Registry

https://ukbec.wordpress.com

Consortium studying the regulation and alternative splicing of gene expression in multiple tissues from human brains. The UKBEC dataset comprises of brains from individuals free of neurodegenerative disorders.

Proper citation: UK Brain Expression Consortium (RRID:SCR_015889) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/ABCDreport

Software application as a simple system to review study progress. Used in ABCD study.

Proper citation: ABCDreport (RRID:SCR_016030) Copy   

•   Source: SciCrunch Registry

https://imagen-europe.com/

Research project examining how biological, psychological, and environmental factors during adolescence may influence brain development and mental health. Using brain imaging and genetics, the project will help develop prevention strategies and improved therapies for mental health disorders in the future., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: IMAGEN (RRID:SCR_016045) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/projects/normalizefov

FSoftware for field-of-view normalization to minimize mismatch in different subjects' images. It aids that streamline analysis of large-scale brain MRI datasets.

Proper citation: NeuroImage Field-of-View Normalization Tool (RRID:SCR_015957) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/DEAP

Web service for data exploration and analysis of the ABCD Study - the largest long-term study of brain development and child health in the United States.

Proper citation: DEAP - Data Exploration and Analysis Portal (RRID:SCR_016158) Copy   

•   Source: SciCrunch Registry

https://nemoarchive.org/

Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility.

Proper citation: NeMOarchive (RRID:SCR_016152) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/vdb/

Virtual resource for neuroscience.

Proper citation: Virtual Digital Brain (RRID:SCR_016265) Copy   

•   Source: SciCrunch Registry