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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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KI Biobank - CEFALO Resource Report Resource Website 1+ mentions |
KI Biobank - CEFALO (RRID:SCR_006034) | CEFALO | biomaterial supply resource, material resource | Saliva taken from participants in a study investigating the association between environmental exposures and brain tumors in children aged 7-19 years and the interaction between these risk factors and genetic polymorphisms, which may confer susceptibility to effects of exogenous agents. Sample types: * Saliva Number of sample donors: 886 (sample collection completed) | cancer, environmental exposure, environment, brain, tumor, child, adolescent, risk factor, genetics, polymorphism, gene, exogenous agent, young human |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Karolisnka Biobank |
Brain tumor, Aging | Swedish Research Council | nlx_151434 | http://ki.se/ki/jsp/polopoly.jsp?d=29332&a=24018&l=en | SCR_006034 | 2026-09-05 06:32:36 | 1 | ||||||
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Centre for Neuro Skills Resource Report Resource Website |
Centre for Neuro Skills (RRID:SCR_006106) | CNS | assessment test provider, material resource | A topical portal and providers of brain injury rehabilitation services. Resources * Pharmacology Guide * Glossary of Brain Injury Terms * Brain Injury Research Articles * Common Brain Injury Assessment Tools / Rating Scale * Certified Continuing Education Courses * Links to Resource Sites | brain, rehabilitation, therapy | Traumatic brain injury, Brain injury | nlx_151579 | SCR_006106 | CNS - Centre for Neuro Skills, Center for Neuro Skills | 2026-09-05 06:32:37 | 0 | ||||||||
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National Alzheimer's Coordinating Center Resource Report Resource Website 50+ mentions |
National Alzheimer's Coordinating Center (RRID:SCR_007327) | NACC | biomaterial supply resource, material resource | A clinical research, neuropathological research and collaborative research database that uses data collected from 29 NIA-funded Alzheimer's Disease Centers (ADCs). The database consists of several datasets, and searches may be done on the entire database or on individual datasets. Any researcher, whether affiliated with an ADC or not, may request a data file for analysis or aggregate data tables. Requested aggregate data tables are produced and returned as soon as the queue allows (usually within 1-3 days depending on the complexity). | alzheimer's disease, brain, clinical, database, disease, human, neuropathological, neuropathology, specimen, tissue, FASEB list |
is listed by: One Mind Biospecimen Bank Listing is related to: Alzheimers Disease Genetics Consortium is related to: Alzheimers Disease Genetics Consortium is related to: National Cell Repository for Alzheimer's Disease has parent organization: University of Washington; Seattle; USA |
Alzheimer's disease, Dementing disorder, Dementia | NIH Blueprint for Neuroscience Research ; NIA U01 AG016976 |
Data are freely available to all researchers | nif-0000-00203 | SCR_007327 | National Alzheimer's Coordinating Center | 2026-09-05 06:32:38 | 54 | |||||
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IBASPM: Individual Brain Atlases using Statistical Parametric Mapping Software Resource Report Resource Website 10+ mentions |
IBASPM: Individual Brain Atlases using Statistical Parametric Mapping Software (RRID:SCR_007110) | IBASPM | software resource, software toolkit | The aim of this work is to present a toolbox for structure segmentation of structural MRI images. All programs were developed in MATLAB based on a widely used fMRI, MRI software package, SPM99, SPM2, SPM5 (Wellcome Department of Cognitive Neurology, London, UK). Other previous works have developed a similar strategy for obtaining the segmentation of individual MRI image into different anatomical structures using a standardized Atlas. Have to be mentioned the one introduced by Montreal Neurological Institute (MNI) that merges the information coming from ANIMAL (algorithm that deforms one image (nonlinear registration) to match previously labelled) and INSECT (Cerebral Tissue Classification) programs for obtaining a suitable gross cortical structure segmentation (Collins et al, 1999). Here both, nonlinear registration and gray matter segmentation processes have been performed through SPM99, SPM2, SPM5 subroutines. Three principal elements for the labeling process are used: gray matter segmentation, normalization transform matrix (that maps voxels from individual space to standardized one) and MaxPro MNI Atlas. All three are combined to yield a good performance in segmenting gross cortical structures. The programs here can be used in general for any standardized Atlas and any MRI image modality. System Requirements: 1. The IBASPM graphical user interface (GUI) runs only under MATLAB 7.0 or higher. The non-graphical version runs under MATLAB 6.5 or higher. 2. Statistical Parametrical Mapping Software SPM2, SPM5 Main Functions: * Atlasing: Main function ( This file contains spm_select script from SPM5 toolbox and uigetdir script from MATLAB 7.0 ). * Auto_Labeling : Computes individual atlas. * Create_SPAMs : Constructs Statistical Probability Anatomy Maps (SPAMs). * Create_MaxProb : Creates Maximum Probability Atlas (MaxPro) using the SPAMs previously computed. * All_Brain_Vol : Computes whole brain volume masking the brain using the segmentation files (if the segmentation files does not exist it segments). * Struct_Vol : Computes the volume for different structures based on individual Atlas previously obtained by the atlasing process. * Vols_Stats : Computes mean and standard deviation for each structure in a group of individual atlases. | segmentation, structural mri, image, label, brain, structure, volume, visualization, atlasing, anatomical structure, probability, statistics, mean, standard deviation, atlas | nlx_144301 | SCR_007110 | Individual Brain Atlases using Statistical Parametric Mapping Software (IBASPM), Individual Brain Atlases using Statistical Parametric Mapping Software | 2026-09-05 06:32:38 | 42 | |||||||||
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Letswave Resource Report Resource Website 10+ mentions |
Letswave (RRID:SCR_016414) | data processing software, data visualization software, software application, software resource, software toolkit | Open source electroencephalogram (EEG) signal processing toolbox to process and visualise EEG/MEG data and other neurophysiological signals. | process, visualise, EEG, MEG, data, neurophysiological, signal, brain, neuroscience | is related to: MATLAB | Free, Available for download, Freely available | https://www.letswave.org/ | SCR_016414 | 2026-09-05 06:30:07 | 27 | |||||||||
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Nutil - Neuroimaging utilities Resource Report Resource Website 10+ mentions |
Nutil - Neuroimaging utilities (RRID:SCR_017183) | Nutil | data processing software, image analysis software, image processing software, software application, software resource, software toolkit | Software toolbox to simplify and streamline mechanism of pre and post processing 2D brain image data. Neuroscience image processing and analysis utilities. Stand alone application that runs on all operating systems. Nutil is part of the QUINT workflow. | neuroscience, 2D, brain, image, data, processing, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Allen Institute for Brain Science has parent organization: University of Oslo; Oslo; Norway works with: VisuAlign |
European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA) and the European Union’s Horizon Europe Programme for Research Infrastructures Grant Agreement No. 101147319 (EBRAINS 2.0). | PMID:32973479 | Free, Available for download, Freely available | https://nutil.readthedocs.io; https://github.com/Neural-Systems-at-UIO/nutil | SCR_017183 | Neuroimaging utilities | 2026-09-05 06:30:08 | 28 | |||||
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Stress Mice Portal Resource Report Resource Website 1+ mentions |
Stress Mice Portal (RRID:SCR_017572) | data or information resource, data set, database, portal, project portal | Sapienza University of Rome and Cineca consortium portal. Used for analyzing published RNAseq transcriptomes obtained from brain of mice exposed to different kinds of stress protocols, to generate database of stress related differentially expressed genes and to identify factors contributing to vulnerability or resistance to stress. Allows to query database of RNAseq data. | Spienza University of Rome, Cineca, RNA seq, transcriptome, data, brain, mouse, stress, gene, expresison | Free, Available for download, Freely available | SCR_017572 | 2026-09-05 06:30:09 | 1 | |||||||||||
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MouseLight Neuron Browser Resource Report Resource Website 10+ mentions |
MouseLight Neuron Browser (RRID:SCR_016669) | software resource, web application | Interactive web platform for anyone to explore, search, filter and visualize the single neuron reconstructions. | explore, search, filter, visualize, single, neuron, reconstruction, mouse, brain |
has parent organization: Janelia Research is provided by: MouseLight Project |
Free, Freely available, Tutorial available, Acknowledgement required | http://mouselight.janelia.org/ | SCR_016669 | Neuron Browser, NeuronBrowser, MouseLight Neuron Browser | 2026-09-05 06:30:21 | 31 | ||||||||
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MRIcron Resource Report Resource Website 1000+ mentions |
MRIcron (RRID:SCR_002403) | MRIcron | data processing software, data visualization software, software application, software resource | Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron. | NIfTI, format, image, viewer, exporting, brain, image, processing, data, bio.tools |
is used by: XFSL: An FSL toolbox is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: neurodebian is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Colour maps for brain imaging has parent organization: University of South Carolina; South Carolina; USA |
PMID:17583985 PMID:11568431 |
BSD License | biotools:MRIcron, nif-0000-00122 | https://sources.debian.org/src/mricron/, http://www.mccauslandcenter.sc.edu/mricro/, http://www.nitrc.org/projects/mricron, http://neuro.debian.net/pkgs/mricron.html, https://bio.tools/MRIcron | SCR_002403 | mricron - magnetic resonance image conversion viewing and analysis | 2026-09-05 06:30:20 | 2312 | |||||
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SenseLab Resource Report Resource Website 10+ mentions |
SenseLab (RRID:SCR_007276) | SenseLab | data or information resource, database, organization portal, portal | The SenseLab Project is a long-term effort to build integrated, multidisciplinary models of neurons and neural systems. It was founded in 1993 as part of the original Human Brain Project, which began the development of neuroinformatics tools in support of neuroscience research. It is now part of the Neuroscience Information Framework (NIF) and the International Neuroinformatics Coordinating Facility (INCF). The SenseLab project involves novel informatics approaches to constructing databases and database tools for collecting and analyzing neuroscience information, using the olfactory system as a model, with extension to other brain systems. SenseLab contains seven related databases that support experimental and theoretical research on the membrane properties: CellPropDB, NeuronDB, ModelDB, ORDB, OdorDB, OdorMapDB, BrainPharmA pilot Web portal that successfully integrates multidisciplinary neurocience data. | neuron, model, olfactory system, brain, disease, neuronal, olfactory |
is related to: Neuroscience Information Framework is related to: International Neuroinformatics Coordinating Facility has parent organization: Yale University; Connecticut; USA is parent organization of: SimToolDB |
Aging | Human Brain Project ; Multidisciplinary University Research Initiative ; NIMH ; NIA ; NICD ; NINDS ; NIDCD RO1 DC 009977 |
nif-0000-00017 | SCR_007276 | SenseLab Project, The SenseLab Project | 2026-09-05 06:30:43 | 41 | ||||||
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ICBM 152 Nonlinear atlases version 2009 Resource Report Resource Website 100+ mentions |
ICBM 152 Nonlinear atlases version 2009 (RRID:SCR_008796) | atlas, data or information resource, reference atlas | Unbiased standard magnetic resonance imaging template brain volume for normal population. These volumes were created using data from ICBM project. 6 different templates are available: * ICBM 2009a Nonlinear Symmetric - template which includes T1w,T2w,PDw modalities, also T2 relaxometry (T2 values calculated for each subject using single dual echo PD/T2 scan), and tissue probabilities maps. Also included lobe atlas used for ANIMAL+INSECT segmentation, brain mask, eye mask and face mask. Intensity inhomogeneity was performed using N3 version 1.10.1. * ICBM 2009a Nonlinear Asymmetric template - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Intensity inhomogeneity was performed using N3 version 1.10.1. Also included brain mask, eye mask and face mask. * ICBM 2009b Nonlinear Symmetric - template which includes only T1w,T2w and PDw modalities. * ICBM 2009b Nonlinear Asymmetric - template which includes only T1w,T2w and PDw modalities. * ICBM 2009c Nonlinear Symmetric - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Also included lobe atlas used for ANIMAL+INSECT segmentation, brain mask, eye mask and face mask. Intensity inhomogeneity was performed using N3 version 1.11. Sampling is different from 2009a template. * ICBM 2009c Nonlinear Asymmetric template - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Intensity inhomogeneity was performed using N3 version 1.11 Also included brain mask, eye mask and face mask.Sampling is different from 2009a template. All templates are describing the same anatomy, but sampling is different. Also, different versions of N3 algorithm produces slightly different tissue probability maps. Tools for using these atlases can be found in the Software section. Viewing the multiple atlas volumes online requires Java browser support. You may also download the templates - see licensing information. | magnetic resonance imaging, brain, human, normal |
is related to: MINC/Atlases is related to: bic-mni-models has parent organization: McConnell Brain Imaging Center |
nlx_144297 | SCR_008796 | , BIC ICBM 152 Nonlinear atlases version 2009 | 2026-09-05 06:30:45 | 278 | |||||||||
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NIHPD Objective 1 atlases (4.5 - 18.5y) Resource Report Resource Website 10+ mentions |
NIHPD Objective 1 atlases (4.5 - 18.5y) (RRID:SCR_008794) | NIHPD Objective 1 atlases (4.518.5y) | atlas, data or information resource, reference atlas | An unbiased standard magnetic resonance imaging template brain volume for pediatric data from the 4.5 to 18.5y age range. These volumes were created using data from 324 children enrolled in the NIH-funded MRI study of normal brain development (Almli et al., 2007, Evans and Group 2006). Tools for using these atlases can be found in the Software section. To view the atlases online, click on the appropriate JIV2 link in the Download section. You can download templates constructed for different age ranges. For each age range you will get an average T1w, T2w, PDw maps normalized between 0 and 100 and tissue probability maps, with values between 0 and 1. Also each age range includes a binary brain mask. | pediatric, human, mri, brain, child, young human | has parent organization: McConnell Brain Imaging Center | Normal brain development, Aging | PMID:20656036 | nlx_144295 | SCR_008794 | BIC NIHPD Objective 1 atlases (4.518.5y), McConnell Brain Imaging Center NIHPD Objective 1 atlases (4.518.5y) | 2026-09-05 06:30:45 | 11 | ||||||
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UBC National Core for Neuroethics Resource Report Resource Website |
UBC National Core for Neuroethics (RRID:SCR_008063) | data or information resource, job resource, organization portal, portal | It is an interdisciplinary research group dedicated to tackling the ethical, legal, policy and social implications of frontier technological developments in the neurosciences. Our objective is to align innovations in the brain sciences with societal, cultural and individual human values through high impact research, education and outreach. The Core''s major research projects are focused on high impact, high visibility areas including the use of drugs and devices for neuroenhancement, ethics in neurodegenerative disease and regenerative medicine research, international and cross-cultural challenges in brain research, neuroimaging in the private sector, and the ethics of personalized medicine, among others. Members of the Core also lead initiatives aside from their research projects. Sponsors: This Core is supported by the University of Brititsh Columbia. | drug, education, ethic, ethical, brain, brain science, human, implication, legal, neurodegenerative disease, neuroenhancement, neuroethics, neuroscience, outreach, policy, regenerative medicine, social, technological development, neuroimaging | has parent organization: University of British Columbia; British Columbia; Canada | nif-0000-10478 | SCR_008063 | University of British Columbia, UBC Neuroethics, National Core for Neuroethics | 2026-09-05 06:30:43 | 0 | |||||||||
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Homer2 Resource Report Resource Website 100+ mentions |
Homer2 (RRID:SCR_009586) | data processing software, image analysis software, software application, software resource | Software matlab scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation. Graphical user interface (GUI) for visualization and analysis of functional near-infrared spectroscopy (fNIRS) data. | Analysis, optical, imaging, fnirs, map, brain, activation, BRAIN Initiative |
is recommended by: BRAIN Initiative is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NIRx2nirs: A NIRx to .nirs data converter |
NCRR P41 RR14075; NIBIB EB025145; NIBIB R01 EB006385 |
Free, Available for download, Freely available | nlx_155773 | http://www.nitrc.org/projects/homer2, https://homer-fnirs.org/ | SCR_009586 | HOMER1, Photon Migration Imaging toolbox | 2026-09-05 06:30:45 | 250 | ||||||
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HERMES Resource Report Resource Website 100+ mentions |
HERMES (RRID:SCR_009584) | HERMES | data processing software, software application, software resource, software toolkit | A toolbox for the Matlab environment designed to study functional and effective brain connectivity from neurophysiological data such as multivariate EEG and/or MEG records. It includes also visualization tools and statistical methods to address the problem of multiple comparisons. This toolbox may be very helpful to all the researchers working in the emerging field of brain connectivity analysis. | clinical neuroinformatics, computational neuroscience, connectivity analysis, directed transfer analysis, eeg, meg, electrocorticography, granger causality, information theory, matlab, partial directed coherence, transfer entropy analysis, connectivity, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Polytechnic University of Madrid; Madrid; Spain |
Ministry of Education of the Community of Madrid NEUROTEU-CM program S2010/BMD-2460; Spanish Ministry of Economy and Competitiveness TEC2012-38453-CO4-01; Spanish Ministry of Economy and Competitiveness TEC2012-38453-CO4-03 |
GNU General Public License | nlx_155770 | http://www.nitrc.org/projects/hermes | SCR_009584 | HERramientas de MEdida de la Sincronizacion | 2026-09-05 06:30:45 | 138 | |||||
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TRACULA Resource Report Resource Website 10+ mentions |
TRACULA (RRID:SCR_013152) | TRACULA | data processing software, software application, software resource | Software tool developed for automatically reconstructing a set of major white matter pathways in the brain from diffusion weighted images using probabilistic tractography. This method utilizes prior information on the anatomy of the pathways from a set of training subjects. By incorporating this prior knowledge in the reconstruction procedure, our method obviates the need for manual intervention with the tract solutions at a later stage and thus facilitates the application of tractography to large studies. The trac-all script is used to preprocess raw diffusion data (correcting for eddy current distortion and B0 field inhomogenities), register them to common spaces, model and reconstruct major white matter pathways (included in the atlas) without any manual intervention. trac-all may be used to execute all the above steps or parts of it depending on the dataset and user''''s preference for analyzing diffusion data. Alternatively, scripts exist to execute chunks of each processing pipeline, and individual commands may be run to execute a single processing step. To explore all the options in running trac-all please refer to the trac-all wiki. In order to use this script to reconstruct tracts in Diffusion images, all the subjects in the dataset must have Freesurfer Recons. | tractography, white matter tract, white matter pathway, diffusion weighted image, diffusion magnetic resonance imaging, white matter, brain, reconstruct, diffusion tensor imaging |
is related to: FreeSurfer has parent organization: Harvard Medical School; Massachusetts; USA |
Aging | NIH Blueprint for Neuroscience Research ; Ellison Medical Foundation ; NIBIB EB008129; NIMH U01-MH093765; NCRR P41-RR14075; NCRR U24-RR021382; NIBIB R01-EB006758; NIA R01-AG022381; National Center for Complementary and Alternative Medicine RC1-AT005728; NINDS R01-NS052585; NINDS R21-NS072652; NINDS R01-NS070963 |
PMID:22016733 | nlx_143919 | SCR_013152 | TRACULA - TRActs Constrained by UnderLying Anatomy, TRACULA: TRActs Constrained by UnderLying Anatomy, TRActs Constrained by UnderLying Anatomy | 2026-09-05 06:30:47 | 17 | |||||
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DPABI Resource Report Resource Website 1000+ mentions |
DPABI (RRID:SCR_010501) | DPABI | data processing software, software application, software resource, software toolkit | Software toolbox for data processing and analysis of brain imaging, evolved from DPARSF (Data Processing Assistant for Resting-State fMRI). | neuroimaging, resting-state fmri, brain, analysis, fmri |
uses: DPARSF has parent organization: RFMRI.ORG |
GNU General Public License | nlx_158469 | SCR_010501 | DPABI: a toolbox for Data Processing & Analysis of Brain Imaging, toolbox for Data Processing and Analysis of Brain Imaging | 2026-09-05 06:30:46 | 1384 | |||||||
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Single Cell Portal Resource Report Resource Website 100+ mentions |
Single Cell Portal (RRID:SCR_014816) | SCP | data or information resource, portal | Portal specializes in visualizing and disseminating single cell data. Allows you to use natural language and faceted search to discover other scientists’ research and share your own findings. Each study includes information on cell types, singular or multiple gene expression, and spatial transcriptomics. Interactive visualizations allow to explore cell clusters and search for related genes. | Single cell data visualization, disseminating single cell data, single cell data, brain, RNA, rna seq, multiple gene expression, spatial transcriptomics, open science |
is used by: BRAIN Initiative is used by: BICCN is related to: BICCN Anatomy and Morphology Project is related to: Allen Institute for Brain Science has parent organization: Broad Institute has organization facet: Terra |
Free, Available for download, Freely available | https://portals.broadinstitute.org/single_cell?utf8=✓&search_terms=e+coli&order=&commit= | SCR_014816 | Single-Cell RNA-Seq Portal for Brain Research | 2026-09-05 06:30:49 | 366 | |||||||
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7T Structural MRI scans ATAG Resource Report Resource Website 1+ mentions |
7T Structural MRI scans ATAG (RRID:SCR_014084) | atlas, data or information resource, data set | Data sets from the atlasing of the basal ganglia (ATAG) consortium, which provides ultra-high resolution 7Tesla (T) magnetic resonance imaging (MRI) scans from young, middle-aged, and elderly participants. They include whole-brain and reduced field-of-view MP2RAGE and T2 scans with ultra-high resolution at a sub millimeter scale. The data can be used to develop new algorithms that help building new high-resolution atlases both in the basic and clinical neurosciences. They can also be used to inform the exact positioning of deep-brain electrodes relevant in patients with Parkinsons disease and neuropsychiatric diseases. | 7t mri, data set, atlas, basal ganglia, structural mri scan, brain, human brain, probabilistic atlas |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Amsterdam; Amsterdam; Netherlands |
Available for download | SCR_014084 | 2026-09-05 06:30:48 | 7 | ||||||||||
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Allen Human Reference Atlas, 3D, 2020 Resource Report Resource Website 1+ mentions |
Allen Human Reference Atlas, 3D, 2020 (RRID:SCR_017764) | atlas, data or information resource, reference atlas | Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas. | Parcellation, adult, human, brain, 3D, atlas, data |
is used by: BICCN has parent organization: Allen Institute works with: Developing Human Brain Atlas version 2 (DHBAv2) |
Allen Institute for Brain Science ; NIMH U01 MH114812 |
Free, Available for download, Freely available | SCR_017764 | 2026-09-05 06:30:54 | 5 |
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