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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Resting State Hemodynamic Response Function Retrieval and Deconvolution
 
Resource Report
Resource Website
1+ mentions
Resting State Hemodynamic Response Function Retrieval and Deconvolution (RRID:SCR_023663) rsHRF software toolkit, software resource Software toolbox for resting state HRF estimation and deconvolution analysis. Matlab and Python toolbox that implements HRF estimation and deconvolution from resting state BOLD signal. Used to retrieve optimal lag between events and HRF onset, as well as HRF shape. Once that HRF has been retrieved for each voxel/vertex, it can be deconvolved from time series or one can map shape parameters everywhere in brain and use it as pathophysiological indicator. Input can be 2D GIfTI, 3D or 4D NIfTI images, but also on time series matrices/vectors. Output are three HRF shape parameters for each voxel/vertex, plus deconvolved time series, and number of retrieved pseudo events. All can be written back to GIfTI or NIfTI images. hemodynamic response function, HRF estimation and deconvolution, resting state BOLD signal, GIfTI images, NIfTI images, brain National Natural Science Foundation of China ;
Fund for Scientific Research-Flanders ;
European Union Horizon 2020 Framework Programme
PMID:34560269 Free, Available for download, Freely available https://github.com/compneuro-da/rsHRF SCR_023663 2026-08-02 09:09:02 3
Brain Connection
 
Resource Report
Resource Website
Brain Connection (RRID:SCR_008315) narrative resource, data or information resource, training material An educational site providing accessible information about how the brain works and how people learn behavior, brain, connection, human, illness, injury, memory, work, language Aging nif-0000-24681 SCR_008315 Brain Connection 2026-08-03 09:33:59 0
SBIA
 
Resource Report
Resource Website
1+ mentions
SBIA (RRID:SCR_013628) SBIA access service resource, service resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 2, 2023. A section of the Penn department of radiology, it is devoted to the development of computer-based image analysis methods and their application to clinical research studies. Image analysis methodologies include image registration, segmentation, population-based statistical analysis, biophysical modeling of anatomical deformations, and high-dimensional pattern classification. Clinical research studies spans a variety of clinical areas and organs, and they include brain diseases such as Alzheimer's disease and schizophrenia, evaluation of treatment effects in large clinical trials, diagnosis of cardiac diseases, and diagnosis prostate, breast and brain cancer. SBIA also performs small animal imaging research aiming to understand brain development in mouse models. It has multiple resources which can be accessed by researcher. effect, alzheimer's, analysis, anatomical, biomedical, biophysical, brain, cancer, breast cancer, cardiac, classification, clinical, computer, deformation, dimensional, disease, method, model, mouse, organ, pattern, prostate, registration, schizophrenia, segmentation, statistical analysis, study, treatment, image has parent organization: University of Pennsylvania; Philadelphia; USA THIS RESOURCE IS NO LONGER IN SERVICE. nif-0000-33052 SCR_013628 The Section for Biomedical Image Analysis, Section for Biomedical Image Analysis 2026-08-03 09:35:21 4
Gene Expression Nervous System Atlas
 
Resource Report
Resource Website
100+ mentions
Gene Expression Nervous System Atlas (RRID:SCR_002721) GENSAT biomaterial supply resource, material resource, organism supplier Gene expression data and maps of mouse central nervous system. Gene expression atlas of developing adult central nervous system in mouse, using in situ hybridization and transgenic mouse techniques. Collection of pictorial gene expression maps of brain and spinal cord of mouse. Provides tools to catalog, map, and electrophysiologically record individual cells. Application of Cre recombinase technologies allows for cell-specific gene manipulation. Transgenic mice created by this project are available to scientific community. molecular neuroanatomy resource, gene expression, cre mice, rodent, adult mouse, development, developing mouse, histology, annotation, central nervous system, in situ hybridization, mutant mouse strain, brain, spinal cord, transgenic bac-egfp reporter, bac-cre recombinase driver mouse line, transgenic mouse, young mouse, genetics, neurology, bac, transgenic, histology, annotation, bioinformatics, FASEB list is used by: NIF Data Federation
is listed by: One Mind Biospecimen Bank Listing
is listed by: re3data.org
is related to: Integrated Brain Gene Expression
is related to: VisiGene Image Browser
is related to: aGEM
has parent organization: Rockefeller University; New York; USA
is parent organization of: Gensat Cre-Mice
NIH ;
NIH Blueprint for Neuroscience Research ;
NINDS N01 NS02331
Free, Freely available nif-0000-00130 http://www.gensat.org/index.html SCR_002721 Gene Expression Nervous System Atlas, GENSAT 2026-08-03 09:31:59 380
National Resource Center for Cephalopods
 
Resource Report
Resource Website
1+ mentions
National Resource Center for Cephalopods (RRID:SCR_002864) NRCC biomaterial supply resource, material resource, organism supplier THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The center serves the biomedical research community's increased needs for alternative invertebrate models by maintaining a consistent year-round supply of live cephalopod mollusks. These animals are suitable for a wide range of physiological and molecular biological investigations. Investigations are being conducted in the area of life history related to improved animal husbandry. Further studies focus on improving culture system design through development of computer automation and innovative water filtration technology. Current biomedical research on cephalopods includes neurophysiology of the giant axon; anatomy and neurophysiology of the equilibrium receptor organ as a comparative model of the vestibular system of invertebrates; chemoreception, basic nutrition, and protein metabolism; cellular receptor function; and brain, behavior, and learning. Services Provided: The center has built a computer-automated, environmentally controlled, recirculating seawater laboratory for the purpose of culturing cephalopods. The tank systems can be used to conduct a variety of experiments never before possible with cephalopods. Visiting researchers have access to dedicated facilities, including wet and dry laboratory space, office space, computer support and accommodations, as well as priority access to all available live animal resources. Off-site investigators can have live animals, dissected animal tissues/body fluids from all life stages, and a variety of molecular reagents (gene libraries and clones) delivered year-round. Staff expertise and an extensive literature library are available. All life stages of the squid (Sepioteuthis lessoniana) and the common cuttlefish (Sepia officinalis) are available year-round from laboratory culture populations. The sepiolid squid (Euprymna scolopes) can also be cultured on request. The squid Lolliguncula brevis is available year-round from local waters; the squids Loligo opalescens, L. pealeii, and L. plei can be obtained seasonally on request. The chambered nautilus, Nautilus pompilius, and Octopus bimaculoides are available on request. Animal costs vary by species and size. Any tissue or body fluid from these animals can also be provided. Fees for special services are negotiated on a case-by-case basis. euprymna scolopes, function, gene, anatomy, animal, axon, behavior, biological, biomedical, brain, cellular, cephalopod mollusk, chemoreception, clone, culture, cuttlefish, invertebrate, inverteprate, laboratory, learning, lolliguncula brevis, metabolism, model, molecular, nautilus pompilius, neurophysiology, nutrition, octopus bimaculoides, organ, physiological, protein, reagent, receptor, research, sepia officinalis, sepiolid squid, sepioteuthis lessoniana, squid has parent organization: University of Texas System; Texas; USA National Institutes of Health ;
National Center for Research Resources ;
Texas Institute of Oceanography
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-25474 SCR_002864 National Resource Center for Cephalopods 2026-08-03 09:32:09 3
Rambo3D
 
Resource Report
Resource Website
Rambo3D (RRID:SCR_006357) Rambo3D d visualization software, software resource, source code A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels. annotation, volume, brain has parent organization: Open Connectome Project nlx_152092 http://openconnectome.github.com/Rambo3D/ SCR_006357 Volume Viewer, VolumeViewer, Remote Annotation and Multichannel Boundary Observer in 3D 2026-08-03 09:32:59 0
KnowledgeSpace
 
Resource Report
Resource Website
1+ mentions
KnowledgeSpace (RRID:SCR_014539) KS portal, knowledge environment resource, data or information resource A community encyclopaedia that links brain research concepts with data, models and literature from around the world. It is an open project where users can participate and contribute to the global research community. brain, neuron, neuroscience, knowledge environment, global, community U.S. Department of Health and Human Services ;
NIH Blueprint for Neuroscience Research ;
NIDA contract HHSN27120080035C
Public, The research community can contribute to this resource, Beta version SCR_014539 Neuroscience Knowledge Space, Knowledge Space 2026-08-04 09:43:27 2
linkRbrain
 
Resource Report
Resource Website
linkRbrain (RRID:SCR_014562) web application, software application, software resource, data management software An online tool for managing and viewing datasets. Data can be viewed in 2D or 3D with activation points as points clouds or projections on the cortex surface. Data can be imported as a NIfTI file or a list of activation peaks and results can be exported as a PDF file. web application, data management software, brain, human, 2d, 3d, activation point, cortex surface Public, Free SCR_014562 LinkRBrain, linkRbrain: online tool for neuroscience 2026-08-04 09:43:28 0
GingerALE
 
Resource Report
Resource Website
100+ mentions
GingerALE (RRID:SCR_014921) data processing software, data analysis software, algorithm resource, software resource, software application Software available from brainmap.org to perform meta-analyses via the activation likelihood estimation (ALE) method. It also includes the transforms for icbm2tal conversions. mri, brain, meta analysis, estimation, icbm2tal, conversion, software, coordinate, algorithm has parent organization: brainmap.org PMID:19172646 Available for download SCR_014921 2026-08-04 09:43:34 491
MultiXplore
 
Resource Report
Resource Website
1+ mentions
MultiXplore (RRID:SCR_014814) data processing software, software application, software resource, data analysis software Graphical user interface that has been implemented as a 3D Slicer plugin (scripted module). It serves to display a corresponding set of cortical regions from functional connectivity matrix in an explorable 3D scene that represents brain anatomical environment. In addition to grey matter regions, MultiXplore automatically finds and extracts deterministic fiber bundles which exist between selected region(s) and adds them to the 3D environment. This feature helps in generating region-based fiber bundles given a desired whole-brain tractography data. gui, graphical user interface, cortical region, functional connectivity matrix, 3d, brain, grey matter, fiber bundle is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Western University; Ontario; Canada
is a plug in for: 3D Slicer
NSERC Available for download SCR_014814 2026-08-04 09:43:32 1
Automatic Tractography-based Parcellation Pipeline
 
Resource Report
Resource Website
1+ mentions
Automatic Tractography-based Parcellation Pipeline (RRID:SCR_014815) ATPP data processing software, software application, software resource, workflow software Integrated pipeline for tractography-based brain parcellation with automatic processing and massive parallel computing. ATPP offers a CLI version for parcellating multiple brain regions and a GUI version for parcellating a specific brain region. " ATPP completely follows the scientific cultural shift to open science, which aims at making scientific research including journal papers, lab notes, data, and, of course, workflow tools, accessible and transparent to all levels of society. ATPP is publicly accessible in Neuroimaging Informatics Tools and Resources Clearinghouse8 (NITRC) (https://www.nitrc.org/projects/atpp). Its source codes are hosted in GitHub9 (https://github.com/haililihai/ATPP_CLI; https://github.com/haililihai/ATPP_GUI), under the GNU generic purpose license version 310 (GPLv3), and are welcome to download and fork. The Digital Object Identifiers (DOIs) providing a persistent way to make digital data easily and uniquely citable was created from Zenodo11 platform with those GitHub repositories (ATPP CLI v2.0.0, doi: https://doi.org/10.5281/zenodo.239702; ATPP GUI v2.0.0, doi: https://doi.org/10.5281/zenodo.239705). " pipeline, integrated pipeline, tractography, brain, parcel, gui, workflow is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Chinese Academy of Sciences; Beijing; China
National Natural Science Foundation of China10.13039/501100001809 911323013162010390581501179 Available for download https://doi.org/10.5281/zenodo.239705, https://doi.org/10.5281/zenodo.239702 https://github.com/haililihai/ATPP_CLI, https://github.com/haililihai/ATPP_GUI SCR_014815 Automatic Tractography-based Parcellation Pipeline (ATPP) 2026-08-04 09:43:31 2
BluePyOpt
 
Resource Report
Resource Website
10+ mentions
BluePyOpt (RRID:SCR_014753) simulation software, software application, software resource An extensible framework for data-driven model parameter optimization that wraps and standardizes several existing open-source tools. BluePyOpt abstracts the optimization and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. It also provides methods for setting up both small- and large-scale optimizations on a variety of platforms. python, optimization, framework, library, brain, model parameter, neuroscience is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) European Union FP7 604102 Acknowledgement requested http://www.nitrc.org/projects/bluepyopt/ SCR_014753 Blue Brain Python Optimization Library, Blue Brain Python Optimisation Library (BluePyOpt), Blue Brain Python Optimisation Library 2026-08-04 09:43:31 27
MRTool
 
Resource Report
Resource Website
1+ mentions
MRTool (RRID:SCR_015956) topical portal, portal, data or information resource Software toolkit for analysis of MR brain imaging data. MRTool runs on Apple computers and PCs and requires SPM12. brain, imaging, neuroimaging, analysis, magnetic, resonance, mr requires: SPM DOI:10.1007/s12021-018-9355-3 Free, Available for download, Runs on MAC OS, Runs on Windows SCR_015956 2026-08-04 09:43:46 8
Marmoset Brain Connectivity Atlas
 
Resource Report
Resource Website
10+ mentions
Marmoset Brain Connectivity Atlas (RRID:SCR_015964) storage service resource, data repository, service resource, atlas, database, data or information resource Brain connectivity atlas to create systematic, digital repository for data on connections between different cortical areas, in primate species. Data repository for connections between different cortical areas in marmoset monkeys. Allows access to data set and enables other interpretations of data, in light of future evolution of knowledge about marmoset cortex. cortex, marmoset, monkey, cerebral, brain, architecture, primate has parent organization: Monash University; Melbourne; Australia
has parent organization: Nencki Institute of Experimental Biology; Warsaw; Poland
works with: Nencki-Monash template
Australian Research Council DP140101968;
Australian Research Council CE140100007;
European Regional Development Fund ;
NIDA R01 DA036400;
NIMH R01 MH087988;
International Neuroinformatics Coordinating Facility
DOI:10.1038/s41467-020-14858-0
PMID:27099164
Free, Freely available http://marmoset.braincircuits.org, http://analysis.marmosetbrain.org SCR_015964 Marmoset Monkey Cerebral Cortex Connectivity Atlas 2026-08-04 09:43:47 26
Common Upper Mammalian Brain Ontology
 
Resource Report
Resource Website
Common Upper Mammalian Brain Ontology (RRID:SCR_003629) CUMBO ontology, data or information resource, controlled vocabulary Ontology of formal definitions (i.e., machine processable) for the types of structures commonly described in neuroanatomy. neuroanatomy, brain is related to: Linked Neuron Data
has parent organization: International Neuroinformatics Coordinating Facility
has parent organization: NeuroLex
nlx_157809 http://neurolex.org/wiki/Cumbo_terms SCR_003629 INCF-CUMBO, Common Upper Mammalian Brain Ontology (CUMBO) 2026-08-04 09:40:57 0
Accelerating Medicines Partnership - Alzheimers
 
Resource Report
Resource Website
Accelerating Medicines Partnership - Alzheimers (RRID:SCR_003742) AMP Alzheimer's, AMP Alzheimer's Disease portal, organization portal, data or information resource, consortium The Alzheimer's disease arm of the Accelerating Medicines Partnership (AMP) that will identify biomarkers that can predict clinical outcomes, conduct a large scale analysis of human AD patient brain tissue samples to validate biological targets, and to increase the understanding of molecular pathways involved in the disease to identify new potential therapeutic targets. The initiative will deposit all data in a repository that will be accessible for use by the biomedical community. The five year endeavor, beginning in 2014, will result in several sets of project outcomes. For the biomarkers project, tau imaging and EEG data will be released in year two, as baseline data becomes available. Completed data from the randomized, blinded trials will be added after the end of the five year studies. This will include both imaging data and data from blood and spinal fluid biomarker studies. For the network analysis project, each project will general several network models of late onset AD (LOAD) and identify key drivers of disease pathogensis by the end of year three. Years four and five will be dedicated to validating the novel targets and refining the network models of LOAD, including screening novel compounds or drugs already in use for other conditions that may have the ability to modulate the likely targets. drug, drug development, biomarker, data sharing, consortium, disease target, drug design, brain tissue, brain, tissue, clinical, neuroimaging, tau, blood, cerebral spinal fluid, eeg, clinical trial, amyloid beta, neurofibrillary tangle is listed by: Consortia-pedia
is related to: Accelerating Medicines Partnership Autoimmune Diseases of Rheumatoid Arthritis and Lupus
is related to: Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D)
is related to: Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D)
is related to: Accelerating Medicines Partnership Autoimmune Diseases of Rheumatoid Arthritis and Lupus
has parent organization: Foundation for the National Institutes of Health
has parent organization: Accelerating Medicines Partnership
NIH ;
Industry partners
nlx_157974 SCR_003742 Accelerating Medicines Partnership - Alzheimer's Disease, Accelerating Medicines Partnership - Alzheimer's, Accelerating Medicines Partnership Alzheimer's Disease 2026-08-04 09:40:59 0
NeuroVault
 
Resource Report
Resource Website
100+ mentions
NeuroVault (RRID:SCR_003806) storage service resource, data repository, service resource Data repository where researchers can publicly store and share unthresholded statistical brain activation maps produced by MRI and PET studies. neuroimaging, fmri, mri, functional mri assay, pet, brain activation map, brain, statistical map, neuroimaging repository uses: NeuroSynth
is used by: NIF Data Federation
is used by: Integrated Datasets
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Stanford Center for Reproducible Neuroscience
International Neuroinformatics Coordinating Facility ;
Max-Planck-Gesellschaft ;
Max Planck Institute for Human Cognitive and Brain Sciences; Leipzig; Germany
Creative Commons Zero License nlx_158106, r3d100012842 http://neurovault.org/api, https://doi.org/10.17616/R31NJMEI SCR_003806 NeuroVault - A public repository of unthresholded brain activation maps 2026-08-04 09:40:59 342
MRC Cognition and Brain Sciences Unit
 
Resource Report
Resource Website
10+ mentions
MRC Cognition and Brain Sciences Unit (RRID:SCR_003818) CBU portal, organization portal, data or information resource, department portal Unit studying human cognition and the brain with about 90 researchers and postgraduate students investigating topics such as attention, emotion, language and memory. They are developing new treatments for depression, improving hearing through cochlear implants, and helping children to overcome memory problems. With a large collection of scientists engaged in both basic and translational research on the mind and brain, the Unit provides an exceptional training and academic environment that benefits postgraduate students and researchers at all levels. A significant part of their research makes use of brain imaging and they have excellent on-site facilities for magnetic resonance imaging (MRI) magnetoencephalography (MEG) and electroencephalography (EEG). They also have clinical facilities at Addenbrooke's Hospital. The Unit has close links both with the hospital and with Cambridge University. cognition, attention, language, memory, emotion, behavior, neuroimaging, computer modelling, brain, depressive disorder, hearing, cochlear implant, child, clinical, mri, magnetoencephalography, eeg, ear, cochlea has parent organization: University of Cambridge; Cambridge; United Kingdom
is parent organization of: CBU Imaging Wiki
is parent organization of: Kymata Atlas
MRC nlx_158118, grid.415036.5, Wikidata: Q5141152, ISNI: 0000 0001 2177 2032 https://ror.org/055bpw879 SCR_003818 Cognition and Brain Sciences Unit 2026-08-04 09:41:00 31
NICHD Brain and Tissue Bank for Developmental Disorders
 
Resource Report
Resource Website
10+ mentions
NICHD Brain and Tissue Bank for Developmental Disorders (RRID:SCR_003601) NICHD BTB biomaterial supply resource, brain bank, material resource, tissue bank The objective of this human tissue repository is to systematically collect, store, and distribute brain and other tissues for research dedicated to the improved understanding, care, and treatment of individuals with developmental disorders. Brain sections are primarily frozen in isopentane / dry ice. Tissues are stored in 10% formalin and frozen at -85 degrees C. Of special interest are individuals with Down syndrome and other chromosomal defects, mitochondrial encephalopathies, phenylketonuria and other aminoacidopathies, maternal PKU, Rett syndrome, leukodystrophies, lysosomal disorders, dyslexia, autism, and other neurodevelopmental disorders. The brain and tissue banks have extensive experience in arranging for the rapid retrieval of tissue upon the death of individuals who die while at home, in hospitals or hospice care. As a special service, the brain and tissue banks are able to assist researchers who are working with patients who intend to donate tissues at the time of their death. Immediately after retrieval of the tissue, the brain and tissue banks will forward needed tissue to the referring investigators and ensure proper storage and cataloging of any additional tissues as part of the brain and tissue banks. The recipient of tissue and the brain and tissue banks are required to sign a Tissue Transfer Agreement before any tissues are transferred. downloadable catalog, tissue, brain, body fluid, cardiovascular system, endocrine system, genital system, gastrointestinal system, hematopoietic system, integumentary, musculo-skeletal, respiratory system, spinal cord, nerve, urinary system, other, rna, frozen, fixed, developmental disorder, down syndrome, chromosomal defect, mitochondrial encephalopathy, phenylketonuria, maternal pku, rett syndrome, dyslexia, autism, neurodevelopmental disorder, aminoacidopathy, pervasive development disorder, leukodystrophy, lysosomal disorder, s syndrome is listed by: One Mind Biospecimen Bank Listing
is listed by: Multiple Sclerosis Discovery Forum
is related to: One Mind Biospecimen Bank Listing
is related to: Multiple Sclerosis Discovery Forum
has parent organization: University of Maryland School of Medicine; Maryland; USA
Developmental disorder, Down syndrome, Chromosomal defect, Mitochondrial encephalopathy, Phenylketonuria, Maternal PKU, Rett Syndrome, Dyslexia, Autism, Neurodevelopmental disorder, Aminoacidopathy, Pervasive Development Disorder, Leukodystrophy, Lysosomal disorder, S syndrome NIH Blueprint for Neuroscience Research contract HHSN275200900011C;
NICHD NO1-HD-9-0011
Public: Tissues are made available to academic researchers and commercial enterprises for basic research. nif-0000-00217 SCR_003601 Eunice Kennedy Shriver NICHD BTB, NICHD Brain and Tissue Bank, NICHD Brain Tissue Bank for Developmental Disorders, NICHD BTB for Developmental Disorders 2026-08-04 09:40:57 38
RFMRI.ORG
 
Resource Report
Resource Website
50+ mentions
RFMRI.ORG (RRID:SCR_004042) R-fMRI Network portal, community building portal, narrative resource, discussion, data or information resource, forum A network for supporting resting-state fMRI (R-fMRI) related studies. It connects R-fMRI researchers (as nodes) by their sharings (as edges). Through the network, ideas, comments, resources, tools, experiences, and data can be shared. Researchers (nodes) with basic neuroscience, methodological, or clinical backgrounds can connect with each other in the network. It also contains a preprint server that allows neuroscientists to share their preprints, comment on each others research and get back valuable information about their experiments from their colleagues. This is based on the arXiv model. Ultimately, the network aims to enhance collaborations among researchers, especially to translate knowledge of basic neuroscience and methodology to clinical applications (bench to bedside). resting-state fmri, fmri, training material, brain is parent organization of: DPARSF
is parent organization of: DPABI
nlx_158470 SCR_004042 The R-fMRI Network - RFMRI.ORG, The R-fMRI Network a network for supporting resting-state fMRI related studies, R-fMRI Network, The R-fMRI Network - a network for supporting resting-state fMRI related studies, R-fMRI Network (RFMRI.ORG), The R-fMRI Network (RFMRI.ORG): A network for supporting resting-state fMRI related studies! 2026-08-04 09:41:03 71

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