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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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nTracer Resource Report Resource Website |
nTracer (RRID:SCR_023032) | data processing software, image processing software, software application, software resource | Software tool as plug-in for ImageJ software. Used for tracing microscopic images. | tracing microscopic images | is a plug in for: ImageJ | Michigan miBRAIN initiative ; Multidisciplinary University Research Initiative Army Research Office ; NIAID R01AI130303; NIGMS F31GM116517; NIGMS P41GM10371; NIH Office of the Director DP2OD006514; NIMH P50MH09427; NIMH R01MH110932; NINDS R01NS076467; NINDS R01NS095367; NINDS U01NS090449; NSF NSF-1707316 |
PMID:30715234 | Free, Available for download, Freely available | SCR_023032 | SciCrunch Registry | 2026-10-17 01:32:28 | 0 | ||||||||
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Hippocampome.org Resource Report Resource Website 10+ mentions |
Hippocampome.org (RRID:SCR_009023) | Hippocampome | data or information resource, database | A curated knowledge base of the circuitry of the hippocampus of normal adult, or adolescent, rodents at the mesoscopic level of neuronal types. Knowledge concerning dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex is distilled from published evidence and is continuously updated as new information becomes available. Each reported neuronal property is documented with a pointer to, and excerpt from, relevant published evidence, such as citation quotes or illustrations. Please note: This is an alpha-testing site. The content is still being vetted for accuracy and has not yet undergone peer-review. As such, it may contain inaccuracies and should not (yet) be trusted as a scholarly resource. The content does not yet appear uniformly across all combinations of browsers and screen resolutions. | interneuron, classification, neuroinformatics, network, hippocampus, neuron, property, morphology, molecular marker, electrophysiology, adult, adolescent, dentate gyrus, ca3, ca2, ca1, subiculum, entorhinal cortex, bio.tools |
is used by: BICCN is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: George Mason University; Virginia; USA |
Normal | Air Force Office of Scientific Research ; Office of Naval Research MURI N00014-10-1-0198; NINDS R01NS39600; NINDS R21NS58816 |
Except otherwise noted, Creative Commons Attribution-ShareAlike License | nlx_152892, biotools:Hippocampome.org | http://www.nitrc.org/projects/hippocampome, https://bio.tools/Hippocampome.org | SCR_009023 | SciCrunch Registry | Hippocampome Portal | 2026-10-17 01:33:28 | 35 | ||||
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Brain RNA-Seq Resource Report Resource Website 100+ mentions |
Brain RNA-Seq (RRID:SCR_013736) | data or information resource, database | Database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of cerebral cortex. Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain. | RNAseq, transcriptome, splicing, data, glia, neuron vascular, cell, cerebral, cortex, mouse, human, brain, FASEB list | has parent organization: Stanford University; Stanford; California | NIGMS T32GM007365; NIMH R01MH09955501; NINDS R01NS08170301 |
PMID:25186741 PMID:26687838 |
Free, Freely available | SCR_017483 | http://www.brainrnaseq.org/ | SCR_013736 | SciCrunch Registry | Barres Brain RNA-Seq | 2026-10-17 01:34:16 | 156 | |||||
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The NINDS Human Cell and Data Repository (NHCDR) Resource Report Resource Website 10+ mentions |
The NINDS Human Cell and Data Repository (NHCDR) (RRID:SCR_016319) | NHCDR | biomaterial supply resource, material resource, tissue bank | Cell sources currently include fibroblasts and/or induced pluripotent stem cells for Alzheimer's Disease, Amyotrophic Lateral Sclerosis (ALS), Ataxia-telangiectasia, Frontotemporal Lobar Degeneration (FTD), Huntington's Disease, Parkinson's Disease, and healthy controls. Cell sources, including isogenic cell lines for current and new diseases covered by the NINDS will be added over the next several years. | Stem, cell, fibroblast, plutipotent, isogenic |
is used by: NIH Heal Project is recommended by: National Library of Medicine is listed by: re3data.org works with: Cellosaurus |
Alzheimer's Disease, Amyotrophic Lateral Sclerosis (ALS), Ataxia-telangiectasia, Frontotemporal Lobar Degeneration (FTD), Huntington's Disease, Parkinson's Disease | NINDS ; NLM |
Restricted | https://nindsgenetics.org/ | SCR_016319 | SciCrunch Registry | NINDS Human Cell and Data Repository (NHCDR) | 2026-10-17 01:33:37 | 21 | |||||
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VALiDATe29 Squirrel Monkey Brain Atlas Resource Report Resource Website 1+ mentions |
VALiDATe29 Squirrel Monkey Brain Atlas (RRID:SCR_015542) | atlas, data or information resource | Atlas was created from MRI scans of squirrel monkey brains. The atlas is currently comprised of multiple anatomical templates, diffusion MRI templates, and ex vivo templates. In addition, the templates are combined with histologically defined cortical labels, and diffusion tractography defined white matter labels. | squirrel brain, squirrel monkey brain, squirrel brain atlas, squirrel mri | has parent organization: Vanderbilt University; Tennessee; USA | NINDS RO1 NS058639; NINDS RO1 NS069909; NINDS RO1 NS078680; NCRR 1S10 RR 17789 |
Available for download | SCR_015542 | SciCrunch Registry | VALiDATe29 Atlas | 2026-10-17 01:33:37 | 1 | ||||||||
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Salk Institute Gene Transfer Targeting and Therapeutics Viral Vector Core Facility Resource Report Resource Website 10+ mentions |
Salk Institute Gene Transfer Targeting and Therapeutics Viral Vector Core Facility (RRID:SCR_014847) | GT3 | access service resource, core facility, service resource | Core facility that provides consultation on the use of viral vector technologies as well as custom design and production services for multiple vector types. The GT3 facilitates the use of these research tools by Salk researchers and others across diverse fields of study such as systems neuroscience, stem cell biology, metabolism, ageing, cancer biology and gene therapy. The GT3 core is a designated Cancer Center Council (C3) core facility. Cancer Center members from participating C3 institutes have preferential rates. | core facility, gene, vector, viral vector, manipulation, gene therapy, cancer, stem cell |
is listed by: ABRF CoreMarketplace has parent organization: Salk Institute for Biological Studies |
NINDS R24 Core Grant ; NEI ; Salk Institute GT3 Core Facility ; NCI CCSG P30 014195; NINDS R24NS092943 |
Restricted | ABRF_1642 | https://coremarketplace.org/?FacilityID=1642&citation=1 | SCR_014847 | SciCrunch Registry | , Salk Institute Gene Transfer Targeting and Therapeutics Viral Vector Core (GT3), Salk Institute Gene Transfer Targeting and Therapeutics Core | 2026-10-17 01:35:45 | 10 | |||||
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University of North Carolina at Chapel Hill School of Medicine Neuroscience Microscopy Core Facility Resource Report Resource Website 50+ mentions |
University of North Carolina at Chapel Hill School of Medicine Neuroscience Microscopy Core Facility (RRID:SCR_019060) | NMC | access service resource, core facility, service resource | Microscopy Core for high resolution imaging and aims to make this technology accessible to neuroscientists and other scientific researchers.Provides advanced systems for cellular and molecular imaging of in vitro and in vivo samples, implements new imaging technologies, particularly related to real time and tissue clearing based imaging of neurodevelopment and neural functions, offers training, consultation, data analysis, image processing, and centralized technical expertise. | USEDit, microscopy, high resolution imaging, neuroscience microscopy, cellular imaging, molecular imaging, in vitro imaging, in vivo imaging, neurodevelopment, neural function, data analysis, image processing, ABRF, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA |
NICHD U54 HD079124; NINDS P30 NS045892 |
Open | ABRF_1052 | https://coremarketplace.org/?FacilityID=1052 | SCR_019060 | SciCrunch Registry | UNC Neuroscience Microscopy Core, University of North Carolina at Chapel Hill UNC Neuroscience Microscopy Core, UNC School of Medicine Neuroscience Microscopy Core Facility | 2026-10-17 01:36:53 | 70 | |||||
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MIRACL Resource Report Resource Website 1+ mentions |
MIRACL (RRID:SCR_020945) | software resource, software toolkit | Automated software resource that combines histologically cleared volumes with connectivity atlases and MRI, enabling analysis of histological features across multiple fiber tracts and networks, and their correlation with in vivo biomarkers.Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI. Open source pipeline for automated registration of mice clarity data to Allen reference atlas, segmentation and feature extraction of mice clarity data in 3D, registration of mice multimodal imaging data to Allen reference atlas, tract or label specific connectivity analysis based on Allen connectivity atlas,comparison of diffusion tensort imaging/tractography, virus tracing using CLARITY and Allen connectivity atlas, statistical analysis of CLARITY and Imaging data, atlas generation and label manipulation. | Image registration, CLARITY, multimodal image registration, connectivity analysis, connectomic data integration, MRI data, connectivity atlases, histological features analysis, mice clarity data |
is related to: Allen Institute for Brain Science works with: Allen Mouse Brain Reference Atlas |
American Society for Neuroradiology ; Bernard and Ronni Lacroute ; Boerger Research Fund for Alzheimer Disease and Neurocognitive Disorders ; GE Healthcare ; HHMI ; Marc Paskin ; NIA R01 AG061120; NIMH R01 MH111444; NINDS R01 NS093057; NINDS R01 NS095985; Stanford Neurosciences Institute ; Stanford Radiology Angel Funds ; U.S. Army Research Laboratory and Defense Advanced Research Projects Agency ; William Randolph Hearst Foundation |
PMID:31796741 | Free, Available for download, Freely available | https://github.com/mgoubran/MIRACL/blob/master/docs/index.rst | SCR_020945 | SciCrunch Registry | Multi modal Image Registration And Connectivity anaLysis | 2026-10-17 01:34:58 | 1 | ||||||
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Duke University of North Carolina Brain Imaging and Analysis Center Core Facility Resource Report Resource Website 1+ mentions |
Duke University of North Carolina Brain Imaging and Analysis Center Core Facility (RRID:SCR_001712) | Duke-UNC BIAC, BIAC | access service resource, core facility, service resource | BIAC strives for excellence in its dual mission of research and service. BIAC faculty members are leaders in imaging methodology development, in analysis techniques, as well as in their application in cognitive and clinical neurosciences. In addition, BIAC offers imaging service to other imaging faculty members on campus and at the University of North Carolina in Chapel Hill. | Imaging methodology development, analysis techniques, cognitive neurosciences application, clinical neurosciences application, imaging service | has parent organization: Duke University; North Carolina; USA | National Institutes of Health ; Autism Speaks ; NINDS |
Restricted | nif-0000-10210 | SCR_001712 | SciCrunch Registry | Duke University of North Carolina Brain Imaging and Analysis Center, Brain Imaging and Analysis Center, Brain Imaging and Analysis Center (BIAC) | 2026-10-17 01:34:50 | 2 | ||||||
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Wellcome-CTC Mouse Strain SNP Genotype Set Resource Report Resource Website 1+ mentions |
Wellcome-CTC Mouse Strain SNP Genotype Set (RRID:SCR_003216) | Wellcome-CTC Mouse Strain SNP Genotype Set | data or information resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Data set of genotypes available for 480 strains and 13370 successful SNP assays that are mapped to build34 of the mouse genome, including 107 SNPs that are mapped to random unanchored sequence 13374 SNPs are mapped onto Build 33 of the mouse genome. You can access the data relative to Build 33 or Build 34. | genome, genotype, snp, chromosome, haplotype, haplotype structure, recombinant inbred mouse strain | has parent organization: Wellcome Trust Centre for Human Genetics | Wellcome Trust ; NCRR R24RR015116; NIGMS R01GM072863; NIAAA U01AA014425; NINDS R01NS049445; NIMH P20-MH 62009; NIAAA U24AA13513 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156947 | SCR_003216 | SciCrunch Registry | 2026-10-17 01:34:46 | 3 | |||||||
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Neurophysiology Imaging Facility Resource Report Resource Website |
Neurophysiology Imaging Facility (RRID:SCR_004080) | NIF | access service resource, core facility, service resource | Neurophysiology imaging core facility that provides anatomical and functional MRI scanning for researchers in the National Institute of Mental Health (NIMH), the National Eye Institute (NEI), and the National Institute for Neurological Disorders and Stroke (NINDS). The shared intramural resource centers on a cutting-edge 4.7T vertical bore scanner dedicated to imaging of nonhuman primates. | mri, fmri, neuroimaging, neurophysiology, brain | has parent organization: National Institute of Mental Health | NIMH ; NINDS ; NEI |
nlx_158530 | SCR_004080 | SciCrunch Registry | Neurophysiology Imaging Facility (NIF) | 2026-10-17 01:34:48 | 0 | |||||||
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Lab Streaming Layer Resource Report Resource Website 50+ mentions |
Lab Streaming Layer (RRID:SCR_017631) | LSL | software application, software resource | System for unified collection of measurement time series in research experiments that handles networking, time synchronization, near real time access as well as optionally centralized collection, viewing and disk recording of data. System for synchronizing streaming data for live analysis or recording. | Synchronizing, streaming, data, live, analysis, recording, collection, time, series, EEG | has parent organization: University of California at San Diego; California; USA | Army Research Laboratory ; NINDS R01 NS047293 |
Free, Freely available | SCR_017631 | SciCrunch Registry | Lab Streaming Layer | 2026-10-17 01:34:55 | 86 | |||||||
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Neuroimaging Informatics Technology Initiative Resource Report Resource Website 100+ mentions |
Neuroimaging Informatics Technology Initiative (RRID:SCR_003141) | NIfTI | knowledge environment, training resource | Coordinated and targeted service, training, and research to speed the development and enhance the utility of informatics tools related to neuroimaging. The initial focus will be on tools that are used in fMRI. If NIfTI proves useful in addressing informatics issues in the fMRI research community, it may be expanded to address similar issues in other areas of neuroimaging. Objectives of NIfTI * Enhancement of existing informatics tools used widely in neuroimaging research * Dissemination of neuroimaging informatics tools and information about them * Community-based approaches to solving common problems, such as lack of interoperability of tools and data * Unique training activities and research career development opportunities to those in the tool-user and tool-developer communities * Research and development of the next generation of neuroimaging informatics tools | neuroimaging, neuroinformatics, technology, service, training, research, mri, fmri, software, algorithm or reusable library, c, computed tomography, developers, information resource, java, matlab, magnetic resonance, nifti, other information resource, pet, spect, software |
is used by: Stark Cross-Sectional Aging is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: GIFTI has parent organization: National Institute of Mental Health is parent organization of: NIfTI Data Format Working Group |
NIH Blueprint for Neuroscience Research ; NIMH ; NINDS |
Free, Freely available | nif-0000-00561 | http://www.nitrc.org/projects/nifti | http://www.bic.mni.mcgill.ca/nifti/ | SCR_003141 | SciCrunch Registry | NIfTI: Neuroimaging Informatics Technology Initiative, Neuroimaging Informatics Technology Initiative (NIfTI) | 2026-10-17 01:33:51 | 349 | ||||
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Patient-Reported Outcomes Measurement Information System Resource Report Resource Website 1000+ mentions |
Patient-Reported Outcomes Measurement Information System (RRID:SCR_004718) | PROMIS | assessment test provider, material resource | Repository of person centered measures that evaluates and monitors physical, mental, and social health in adults and children. | adult, child, assessment, clinical, anger, pain, fatigue, physical function, depression, anxiety, social function, patient reported outcome, health, measure |
is recommended by: National Library of Medicine has parent organization: University of Washington; Seattle; USA |
NCCIH ; NCI ; NHLBI ; NIAMS ; NIA ; NIDA ; NIDCD ; NIDDK ; NIMH ; NINDS ; NINR ; OD |
nlx_143881 | http://www.healthmeasures.net/index.php?option=com_content&view=category&layout=blog&id=71&Itemid=817 | SCR_004718 | SciCrunch Registry | PROMIS, Patient Reported Outcomes Measurement Information System | 2026-10-17 01:33:50 | 3303 | ||||||
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FMRIB’s Integrated Registration and Segmentation Tool Resource Report Resource Website 1+ mentions |
FMRIB’s Integrated Registration and Segmentation Tool (RRID:SCR_024921) | FIRST | data analysis software, data processing software, image analysis software, registration software, segmentation software, software application, software resource | Software model based segmentation and registration tool. Used for segmentation of sub-cortical structures. Introduces basic segmentation and vertex analysis for detecting group differences. | Functional Magnetic Resonance Imaging of the Brain, segmentation, registration, volumetric segmentation, performing vertex analysis, |
is related to: Multimodal Image Segmentation Tool is a plug in for: FSL |
NCRR P41 RR14075; NCRR R01 RR16594; NIDA R01 DA017905; NIMH K01 MH01798; NIMH K08 MH01573; NINDS R01 NS052585 |
PMID:21352927 | Free, Freely available | SCR_024921 | SciCrunch Registry | , Functional Magnetic Resonance Imaging of the Brain's Integrated Registration and Segmentation Tool | 2026-10-17 01:38:34 | 7 | ||||||
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Keypoint MoSeq Resource Report Resource Website 10+ mentions |
Keypoint MoSeq (RRID:SCR_025032) | software resource, source code | Software application as machine learning-based platform for identifying behavioral modules from keypoint data without human supervision. Package provides tools for fitting MoSeq model to keypoint tracking data. Used to infer pose dynamics with keypoint data in addition to behavioral syllables. | OpenBehavior, infer pose dynamics, keypoint data, identifying behavioral modules, keypoint tracking data, parsing behavior, linking point tracking to pose dynamics, | has parent organization: Harvard University; Cambridge; United States | Alfred P. Sloan Foundation ; NIA RF1AG073625; NINDS F31NS113385; NINDS F31NS122155; NINDS R01NS114020; NINDS U19NS113201; NINDS U24NS109520; Salk Collaboration Grant ; Simons Collaboration on Plasticity and the Aging Brain ; Simons Collaboration on the Global Brain ; Simons Foundation Autism Research Initiative |
DOI:10.1101/2023.03.16.532307 | Free, Available for download, Freely available | SCR_025032 | SciCrunch Registry | 2026-10-17 01:37:20 | 12 | ||||||||
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E-Scope Resource Report Resource Website 1+ mentions |
E-Scope (RRID:SCR_025396) | instrument resource, software resource, source code | Miniaturized calcium imaging microscope with integrated dense electrode technology for synchronous acquisition of neural activity across distant regions of the brain. Device based off open-sourced UCLA Miniscope to synchronously measure single cell activity at or near spike-time resolution across distant brain regions in freely behaving mice. Used to perform calcium imaging, with dense electrode electrophysiological recording, allowing simultaneous recordings from two remote brain regions in freely behaving mouse. | OpenBehavior, miniatured microscope, calcium imaging microscope, microscope, synchronous acquisition, freely behaving mice, neural activity, brain distant regions, synchronously measure single cell activity, |
is listed by: OpenBehavior is related to: UCLA Miniscope project |
NICHD P50HD103577; NINDS 1R61NS119708; NINDS R01NS090930; NINDS U01NS122124; NSF NeuroNex Award |
PMID:37066345 | Free, Available for download, Freely available | http://miniscope.org/index.php/Main_Page, https://edspace.american.edu/openbehavior/?s=E-Scope | SCR_025396 | SciCrunch Registry | 2026-10-17 01:37:26 | 3 | |||||||
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Annotation Comparison Explorer Resource Report Resource Website 1+ mentions |
Annotation Comparison Explorer (RRID:SCR_026496) | ACE | software resource, web application | Web application for comparing cell type assignments and other cell-based annotations (e.g., donor demographics, anatomic locations, batch variables, and quality control metrics). Used for connecting brain cell types across studies of health and Alzheimer's Disease. | comparing cell type assignments, cell-based annotations, connecting brain cell types, |
has parent organization: Allen Institute is organization facet of: BRAIN Initiative Cell Atlas Network |
NIA U19AG060909; NINDS U24NS133077 |
PMID:39990500 | Free, Freely available | github.com/AllenInstitute/ACE | SCR_026496 | SciCrunch Registry | Annotation Comparison Explorer (ACE) | 2026-10-17 01:37:12 | 1 | |||||
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Borzoi Resource Report Resource Website 1+ mentions |
Borzoi (RRID:SCR_026619) | software resource, software toolkit, source code | Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences. | Borzoi models access, convolutional neural networks, predict RNA-seq coverage, | Common Fund of the Office of the Director ; NCI ; NHGRI ; NHLBI ; NIDA ; NIMH ; NINDS |
PMID:39779956 | Free, Available for download, Freely available | SCR_026619 | SciCrunch Registry | 2026-10-17 01:37:16 | 2 | |||||||||
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Diffusion-Model Resource Report Resource Website 1+ mentions |
Diffusion-Model (RRID:SCR_027942) | software resource, source code | Software code for simulating diffusion in brain extracellular space images. | simulating diffusion, brain, extracellular space, images | NINDS R01NS130759; NSF ; Spanish Government |
PMID:41279667 | Free, Available for download, Freely available | SCR_027942 | SciCrunch Registry | , Diffusion Flux, DifFlux, Diffusion Flux Model | 2026-10-17 01:39:23 | 1 |
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