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http://dabi.loni.usc.edu/

Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves.

Proper citation: Data Archive BRAIN Initiative (RRID:SCR_017114) Copy   

•   Source: SciCrunch Registry

https://github.com/Neural-Systems-at-UIO/MeshView-for-Brain-Atlases

Web application for real time 3D display of surface mesh data representing structural parcellations and generation of user defined cut planes from volumetric atlases.

Proper citation: MeshView (RRID:SCR_017222) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/pubmed/28653482

Software tool to facilitate tractography based deep brain stimulation (DBS) electrode targeting within patient specific stereotactic coordinate system used in operating room.

Proper citation: StimVision (RRID:SCR_017457) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/tdtdecodingtoolbox/

Software Matlab toolbox for multivariate analysis of functional and structural MRI data. Software package for multivariate analyses of functional imaging data.

Proper citation: The Decoding Toolbox (RRID:SCR_017424) Copy   

•   Source: SciCrunch Registry

https://usa.brainreader.net

Software application as image segmentation tool. Brain volumetry assessment software. Processes MRI scans and provides self explanatory patient report with total brain volume, hippocampal volume and volumetric data on key segments of brain measured against healthy database.

Proper citation: Neuroreader (RRID:SCR_017309) Copy   

•   Source: SciCrunch Registry

https://github.com/bheAI/MonkeyCBP_CLI

Software toolbox for connectivity based parcellation of monkey brain. Integrated pipeline realizing tractography based brain parcellation with automatic processing and massive parallel computing. Highly automated process and high throughput performance supported by GPU option makes toolbox ready to be used by research community.

Proper citation: MonkeyCBP (RRID:SCR_017640) Copy   

•   Source: SciCrunch Registry

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

Software tool as deep neural network for predicting FreeSurfer segmentations of structural MRI volumes. This tool is implemented as both Docker and Singularity containers. Used for brain parcellation and uncertainty estimation.

Proper citation: Knowing what you know (kwyk) - Bayesian Brain Parcellation (RRID:SCR_017470) Copy   

•   Source: SciCrunch Registry

https://www.biomax.com/neuroxm

Software toolkit for semantic integration of multi-modal brain data. It is used to collect, structure, connect, analyze and re-use brain data.

Proper citation: NeuroXM Brain Science Suite (RRID:SCR_016372) Copy   

•   Source: SciCrunch Registry

https://github.com/CPernet/brain_colours

Software tool as a perceptually uniform color maps. Used in scientific literature to reflect data of brain imaging.

Proper citation: Colour maps for brain imaging (RRID:SCR_016715) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/anocva/index.html

Software R package as a nonparametric statistical test to compare clustering structures with applications in functional magnetic resonance imaging data (fMRI). Used for analysis of cluster variability in the diagnosis of neuropsychological disorders.

Proper citation: ANOCVA (RRID:SCR_016719) Copy   

•   Source: SciCrunch Registry

https://www.janelia.org/project-team/mouselight

Software imaging platform to generate datasets of whole mouse brains imaged at submicron resolution that allow reconstructions of complete axonal arbors of individual neurons across the entire mouse brain.

Proper citation: MouseLight Project (RRID:SCR_016668) Copy   

•   Source: SciCrunch Registry

https://github.com/vaklip/rsfmri_fconn

Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity.

Proper citation: rsfMRI_fconn calculation (RRID:SCR_016591) Copy   

•   Source: SciCrunch Registry

https://github.com/afids

Open framework for evaluating correspondence between brain images and teaching neuroanatomy.

Proper citation: AFIDs (RRID:SCR_016623) Copy   

•   Source: SciCrunch Registry

http://www.callisto-science.org/NSI/Neuroscience_Image_Database/Rat_Brain_Atlas.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 27,2025. Compact 3rd edition of The Rat Brain Atlas of Paxinos & Watson published in 1997, it is the most widely used stereotaxic reference system for rat brain. The illustrations and nomenclature of the atlas have become standard tools used by almost all research neuroscientists who deal with anatomy, physiology, or function. It has been subsequently updated, with the 6th edition being the most recent. The 3rd edition is the most recent one available online for free. The program runs in Adobe Acrobat Reader.

Proper citation: Rat Brain Atlas of Paxinos and Watson (RRID:SCR_006369) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/ServicesAtlases/Macaque

A reference atlas of standard macaque monkey magnetic resonance images. The template brain volume that offers a common stereotaxic reference frame to localize anatomical and functional information in an organized and reliable way for comparison across individual macaque monkeys and studies. We have used MRI volumes from a group of 25 normal adult macaque monkeys (18 Macaca fascicularis, 7 Macaca mulatta) to create the individual atlas. Thus, the atlas does not rely on the anatomy of a single subject, but instead depends on nonlinear normalization of numerous macaque brains mapped to an average template image that is faithful to the location of anatomical structures. Tools for registering a native MRI to the MNI macaque atlas can be found in the Software section. Viewing the atlas and associated volumes online requires Java browser support. Additionally, you may download the atlas and associated files in your chosen format.

Proper citation: McConnell Brain Imaging Center MNI Macaque Atlas (RRID:SCR_005265) Copy   

•   Source: SciCrunch Registry

http://neurosynth.org

Platform for large-scale, automated synthesis of functional magnetic resonance imaging (fMRI) data extracted from published articles. It''s a website wrapped around a set of open-source Python and JavaScript packages. Neurosynth lets you run crude but useful analyses of fMRI data on a very large scale. You can: * Interactively visualize the results of over 3,000 term-based meta-analyses * Select specific locations in the human brain and view associated terms * Browse through the nearly 10,000 studies in the database Their ultimate goal is to enable dynamic real-time analysis, so that you''ll be able to select foci, tables, or entire studies for analysis and run a full-blown meta-analysis without leaving your browser. You''ll also be able to do things like upload entirely new images and obtain probabilistic estimates of the cognitive states most likely to be associated with the image.

Proper citation: NeuroSynth (RRID:SCR_006798) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/

Center dedicated to understanding and treatment of neurological diseases by creating and using imaging methods to study human nervous system. Dedicated to research imaging of human brain. Brain structure is imaged using anatomical Magnetic Resonance Imaging (aMRI) while brain physiology is imaged using Positron Emission Tomography (PET), Magnetic Resonance Spectroscopy (MRS), functional MRI (fMRI) and magnetoencephalography (MEG). BIC maintains linkages with clinical, clinical research and basic research communities within Montreal Neurological Institute (MNI), McGill University and has collaborations across Quebec, Canada, USA and internationally.

Proper citation: McConnell Brain Imaging Center (RRID:SCR_008364) Copy   

•   Source: SciCrunch Registry

http://www.uab.edu/cnc

The overall mission of the Comprehensive Neuroscience Center (CNC) is to promote and support interdisciplinary neuroscience research, clinical care and education at UAB. Despite significant advances over the last 15 years in understanding many basic neurological processes, development of more effective treatments for neurological and psychiatric diseases have been identified as the largest and fastest growing unmet medical need in this country. The institutions that can most rapidly and creatively establish the necessary neuroscience initiatives to facilitate the translation of basic research discoveries into effective therapies will be positioned to lead neurological and psychiatric disease research into the future. The Center integrates a variety of disciplines, including neurology, psychiatry, neurobiology, neurosurgery, psychology, vision science, and biomedical engineering. Faculty from the Schools of Medicine, Optometry, Social and Behavioral Sciences, Dentistry, Engineering, Health Professions, and Public Health are affiliated with the Center. The need to address neuroscience research is great: one in three Americans are affected by nervous system diseases including brain and spinal cord injury, dementing illnesses, schizophrenia, depression, movement disorders, multiple sclerosis, and autism. The burden of these diseases has an estimated economic cost of 500 billion per year in the United States. Center Research: The CNC serves as a vital center for neuroscience research at UAB and oversees six thematic programs of investigation: neurodevelopment and neurogenetics, neurodegeneration and experimental therapeutics, neuroregeneration and plasticity, behavioral and cognitive health, glial biology in medicine, and neuroimaging. The CNC helps coordinate the efforts of multiple neuroscience related centers at UAB, such as the Center for Glial Biology in Medicine, the Evelyn F. McKnight Brain Institute, the Civitan International Research Center, and the Alzheimers Disease Research Center. By interacting directly with these centers and establishing coalitions of centers and neuroscience subdisciplines, the CNC aids the UAB neuroscience community in meeting the challenges of modern neuroscience investigation. The CNC builds on other recent advances in neuroscience at UAB, including an 8.6 million grant from the National Institutes of Health to establish the Alabama Neuroscience Blueprint Core Center Facility awarded in September 2006. The Neuroscience Blueprint establishes research infrastructure on campus that is shared by investigators from institutions across Alabama and the Southeast. UAB has also added dynamic new leadership in the neuroscience fields including the following new chairs: Ray L. Watts, MD, Neurology (from Emory University); David Sweatt, PhD, Neurobiology (from Baylor College of Medicine); and James Meador-Woodruff, MD, Psychiatry (from the University of Michigan).

Proper citation: UAB Comprehensive Neuroscience Center (RRID:SCR_007195) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/ServicesAtlases/Cyno

A reference atlas of cynomolgus macaque monkey magnetic resonance images. The template brain volume that offers a common stereotaxic reference frame to localize anatomical and functional information in an organized and reliable way for comparison across individual cynomolgus monkeys and studies. We have used MRI volumes from a group of 18 normal adult cynomulgus monkeys (Macaca fascicularis) to create the individual atlas. Thus, the atlas does not rely on the anatomy of a single subject, but instead depends on nonlinear normalization of numerous cynomolgus monkey brains mapped to an average template image that is faithful to the location of anatomical structures. Tools for registering a native MRI to the cynomolgus macaque atlas can be found in the Software section. Viewing the atlas and associated volumes online requires Java browser support. Additionally, you may download the atlas and associated files in your chosen format.

Proper citation: McConnell Brain Imaging Center MNI Cynomolgus Macaque Atlas (RRID:SCR_008793) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj2

An unbiased magnetic resonance imaging template brain volume for pediatric data from birth to 4.5y age range. These volumes were created using 317 scans from 108 children enrolled in the NIH-funded MRI study of normal brain development (Almli et al., 2007, Evans and Group 2006). Templates are constructed for different age ranges. Each age range includes an average T1w, T2w, PDw maps normalized between 0 and 100. Also each age range includes a binary brain mask. Tools for using these atlases can be found in the Software section.

Proper citation: NIHPD Objective 2 atlases (birth - 4.5 years) (RRID:SCR_008795) Copy   

•   Source: SciCrunch Registry