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http://sig.biostr.washington.edu/projects/MindSeer/index.html

A cross-platform application for 3D brain visualization for multi-modality neuroimaging data written in Java/Java3D, that runs in both standalone and client-server mode. It supports basic data management capabilities, visualization of 3D surfaces (SPM's output or OFF files), volumes (Analyze, NIFTI or Minc) and label sets. MindSeer has 2 different modes: # Client/Server is designed to allow users to visualize data that is stored centrally and enhance collaboration. # Standalone mode is available to view local data and is built for more performance than Client/Server Both modes have the same interface and support the same features. It has a modular architecture and is designed to be extensible. Requirements: # Java 5.0 or above. # Java Web Start. # Java3D (installed automatically by Web Start).

Proper citation: MindSeer (RRID:SCR_003019) Copy   

•   Source: SciCrunch Registry

http://www.mricro.com

Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.

Proper citation: MRIcron (RRID:SCR_002403) Copy   

•   Source: SciCrunch Registry

http://www.neuro.uni-jena.de/cat/

Software toolbox as extension to SPM12 to provide computational anatomy. This covers diverse morphometric methods such as voxel based morphometry, surface based morphometry, deformation based morphometry, and region or label based morphometry.

Proper citation: Computational Anatomy Toolbox for SPM (RRID:SCR_019184) Copy   

•   Source: SciCrunch Registry

https://voxelmorph.net

Software tool for joint surface based registration and atlas construction of brain geometry and function.Cortical registration framework that jointly models mismatch between geometry and function while simultaneously learning unbiased population specific atlas.

Proper citation: JOSA (RRID:SCR_024756) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT

Sotware automated robust and accurate tool for linear (affine) intra- and inter-modal brain image registration.

Proper citation: FMRIB's Linear Image Registration Tool (RRID:SCR_024922) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/verbena

Software tool for quantification of perfusion and other haemodynamic parameters from Dynamic Susceptibility Contrast perfusion MRI of the brain.

Proper citation: VERBENA (RRID:SCR_024919) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/XTRACT

Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain.

Proper citation: XTRACT (RRID:SCR_024933) Copy   

•   Source: SciCrunch Registry

https://marmotgraph.org

Knowledge graph system developed for managing and organizing rich metadata objects, initially for the Human Brain Project (HBP) and now extended to be a more generic, domain-agnostic solution. It is associated with CSCS (Swiss National Supercomputing Centre) and aims to provide a comprehensive toolset and API for working with knowledge graphs.

Proper citation: MarmotGraph (RRID:SCR_027452) Copy   

•   Source: SciCrunch Registry

https://imaging.uci.edu/fibre/

Facility for Imaging and Brain Research houses 3T Siemens Prisma scanner, mock scanner, and data analysis facilities. Research dedicated MRI scanning facility designed to suit wide range of basic and translational research programs by researchers across the UCI campus and beyond.

Proper citation: University of California at Irvine FIBRE Core Facility (RRID:SCR_027777) Copy   

•   Source: SciCrunch Registry

https://bican.mccarrolllab.org/app/bican?_inputs_&geneList=%22XIST%20PDE10A%20%20PENK%20PDYN%22&navbarPage=%22panelGeneExpr%22&plotExpressionButton=0&exprPlotUseCommonYScale=true&cellTypeSelector=%5B%22MSN%22%2C%22MSN_D1%22%2C%22MSN_D2%22%2C%22MSN_D1_matrix%22%2C%22MSN_D2_matrix%22%2C%22MSN_D1_striosome%22%2C%22MSN_D2_striosome%22%5D&exprPlotRegionSelector=%22Pu%22&GeneExprPlot_hover=null

Project provides data currently generated with support from the NIH Brain Initiative Cell Atlas Network (BICAN). Broad Institute collaboration supported by the NIH BRAIN Initiative, to create comprehensive atlas of cellular variation in the healthy human brain. It maps data from millions of cells across diverse individuals to understand how brain biology differs, helping researchers distinguish healthy variation from disease states.

Proper citation: Human Brain Variation Project (RRID:SCR_028065) Copy   

•   Source: SciCrunch Registry

https://github.com/SCANDAN-Team/SCANDAN-DICOM-labelling

Software tool for rules for DICOM tag based labelling. Regular expression used during the SCANDAN project to label MRI scans based on DICOM tag.

Proper citation: SCANDAN-DICOM-labelling (RRID:SCR_028365) Copy   

•   Source: SciCrunch Registry

http://www.biausa.org/

The country''s oldest and largest nationwide brain injury advocacy organization. We are dedicated to increasing access to quality health care and raising awareness and understanding of brain injury through advocacy, education and research. With a nationwide network of more than 40 chartered state affiliates and hundreds of local chapters and support groups, we provide help, hope and healing for individuals who live with brain injury, their families and the professionals who serve them. Brain injury is not an event or an outcome. It is the start of a misdiagnosed, misunderstood, under-funded neurological disease. Individuals who sustain brain injuries must have timely access to expert trauma care, specialized rehabilitation, lifelong disease management and individualized services and supports in order to live healthy, independent and satisfying lives.

Proper citation: Brain Injury Association of America (RRID:SCR_006639) Copy   

•   Source: SciCrunch Registry

http://www.abta.org/

Founded in 1973, the American Brain Tumor Association (ABTA) was the first national nonprofit organization dedicated solely to brain tumors. For nearly 40 years, the Chicago-based ABTA has provided critical funding to researchers working toward breakthroughs in brain tumor diagnosis, treatment and care, and is the only national organization providing comprehensive resources and serving the complex supportive care needs of brain tumor patients and caregivers from diagnosis through treatment and beyond.

Proper citation: American Brain Tumor Association (RRID:SCR_006649) Copy   

•   Source: SciCrunch Registry

http://www.proteinatlas.org/

Open access resource for human proteins. Used to search for specific genes or proteins or explore different resources, each focusing on particular aspect of the genome-wide analysis of the human proteins: Tissue, Brain, Single Cell, Subcellular, Cancer, Blood, Cell line, Structure and Interaction. Swedish-based program to map all human proteins in cells, tissues, and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome.

Proper citation: The Human Protein Atlas (RRID:SCR_006710) Copy   

•   Source: SciCrunch Registry

http://infocenter.nimh.nih.gov/il/public_il/

Database of photographs and illustrations of general biomedical research and research tools, mental health specific research, and treatment related images that are available, copyright free, to the public at no cost. Many images are available in low, medium, and high resolutions. Formats include jpg, gif, and png. NIMH images may not be used to state or imply the endorsement by NIMH or by an NIMH employee of a commercial product, service, or activity, or use in any other manner that might mislead. No fee is charged for using the images. However, credit must be given to the National Institute of Mental Health, National Institutes of Health, Department of Health and Human Services unless otherwise instructed to give credit to the photographer or other source., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NIMH Image Library (RRID:SCR_005588) Copy   

•   Source: SciCrunch Registry

http://www.jsmf.org/

Supports research and scholarship to improve the quality of life by providing funding for grants in three program areas: studying complex systems, understanding human cognition, and mathematical and complex systems approaches for brain cancer. Types of awards include Fellowship Awards, Scholar Awards, and Collaborative Awards. * Studying Complex Systems: This program supports scholarship and research directed toward the development of theoretical and mathematical tools that can be applied to the study of complex, adaptive, nonlinear systems. It is anticipated that research funded in this program will address issues in fields such as biology, biodiversity, climate, demography, epidemiology, technological change, economic development, governance, or computation. * Understanding Human Cognition: This program supports research studying how neural systems are linked to and support cognitive functions and how cognitive systems are related to an organism's (preferably human) observable behavior. Studies with model organisms should justify why such models were selected and how data obtained from models advances our understanding of human cognition. * Mathematical & Complex Systems Approaches for Brain Cancer: (Collaborative Activity Awards grant type only.) Despite some recent cause for optimism for advancing the clinical treatment of brain cancers, for many patients brain tumor remains a devastating diagnosis. Progress against this disease has been stymied by limited understandings of the molecular, metabolic, and physiological characteristics of human brain cancers across multiple temporal and spatial scales and by the failure of many preclinical models to predict patient responses.

Proper citation: James S. McDonnell Foundation (RRID:SCR_006341) Copy   

•   Source: SciCrunch Registry

http://www.sbtf.org/home.html

Founded in 1995, the Southeastern Brain Tumor Foundation (SBTF), a 501c3 not-for-profit charitable foundation, is devoted to improve the quality of life for brain tumor patients and their families. By offering information, education and support services, we aspire to instill hope, knowledge and comfort to all involved. The Southeastern Brain Tumor Foundation also raises funds for research and medical personnel so that a cure can be found. For over a decade, the SBTF has become a well-known fundraising entity supporting critical, cutting edge brain tumor research at major medical centers in the Southeast. Our annual Race for Research held in Atlanta, Georgia each summer, is our main fundraising event popular throughout Atlanta and the surrounding metropolitan area and has funded over $1.2 million dollars in research grants to leading researchers at major medical centers throughout the Southeast over the past decade. We are proud of our dedicated, all volunteer Board of Directors who meet monthly. Our Board is a diverse group comprised of individuals who''ve been touched by brain tumors in many different ways. Ranging from patients and family members to healthcare professionals; we are all committed to promoting the awareness of brain tumors in the community, communicating with patients and families and raising critical funds for research grants furthering advancements in the treatment of brain tumors. Our monthly support group, lead by a nurse practitioner, welcomes patients and their families to sit side by side with each other, share their experiences, communicate and receive support. As a neurosurgeon-scientist focused on the treatment of patients with brain tumors, I am committed to advancing the mission of SBTF forward in the fight against brain tumors. Our ability to serve the brain tumor community is dependent on each of you. Whether you support us with a financial donation in our fundraising efforts or with your time as a volunteer, each of you are a vital and integral part of our success and we thank you.

Proper citation: Southeastern Brain Tumor Foundation (RRID:SCR_004768) Copy   

•   Source: SciCrunch Registry

http://www.meduniwien.ac.at/kin/index.html

The (Clinical) Institute of Neurology (IN) of the Medical University Vienna was founded in 1882 by Heinrich Obersteiner. It is the oldest institution embracing the multidisciplinarity of neurosciences and has served as model for the establishment of similarly designed institutions in many countries. The original location of the then Neurological Institute in Vienna was at Schwarzspanierstrasse. Since 1993, IN is located in the Vienna General Hospital in top-class laboratory facilities. IN is committed to its proud tradition as Obersteiner Institute and to a promising future of a nationally and internationally leading institution in the clinical neurosciences. Our work aims to translate the understanding of nervous diseases to the development of novel therapeutics and diagnostics. IN''''s tasks include diagnostic patient service, research and graduate / postgraduate teaching in neuropathology, neurochemistry, and neuro-molecular biology in an integrated way. Neuropathology is a recognized medical specialty in Austria. It analyzes structural changes of nervous tissues in disease. Diagnostic neuropathology makes use of most modern morphological techniques applied to diseased central, peripheral and vegetative nervous tissues and fluids, and muscle. Neuropathological diagnoses are a basis for disease classification and rational therapies. Neurodegenerative disorders, in particular prion diseases, virus diseases affecting the nervous system, and brain tumors (neuro-oncology) are research priorities. In the highly publicized area of prion diseases, IN has developed into a national and international center of excellence and expertise that leads several European, EU-funded networks in prion research. As an indispensable asset, the IN possesses a large brain bank that has systematically collected neuropathological specimens since 1948. Most samples are fixed and paraffin-embedded tissue only, but in a part of neurosurgical, nerve and muscle biopsies and autopsies, also fresh tissue is obtained, frozen and stored at -80 degrees C. Occasionally blood and CSF are also available. The unique neuropathological collection of histological slides, paraffin blocks and formol-fixed nervous tissues now comprises about 16.000 brain autopsies, 30.000 neurosurgical and 7.500 nerve/muscle biopsies. Also a number of cell cultures have been stored, mainly fibroblasts from patients with rare neurometabolic diseases, and primary cultures of brain tumors. IN participates in the EU-supported European Network of Brain Banks BrainNet Europe.

Proper citation: Medical University of Vienna Institute of Neurology (RRID:SCR_005030) Copy   

•   Source: SciCrunch Registry

http://www.braintumorfunders.org/

The Brain Tumor Funders'' Collaborative is a partnership among five private philanthropic and advocacy organizations: American Brain Tumor Association, Brain Tumour Foundation of Canada, Children''s Brain Tumor Foundation, James S. McDonnell Foundation, and Sontag Foundation. This Collaborative promotes research directly relating to brain tumors and offers grants to professors and institutions to conduct research.

Proper citation: Brain Tumor Funders Collaborative (RRID:SCR_005104) Copy   

•   Source: SciCrunch Registry

https://alleninstitute.org/

Non profit bioscience research organization in Seattle, Washington dedicated to accelerating research globally and sharing that data within the science community. Allen Institute for Brain Science, Allen Institute for Cell Science, Allen Institute for Immunology, and The Paul G. Allen Frontiers Group are four divisions of this Institute with commitment to open science model within its research institutes.

Proper citation: Allen Institute (RRID:SCR_005435) Copy   

•   Source: SciCrunch Registry