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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Molecular Brain: Transcription Profiles of Mouse and Human Brains
 
Resource Report
Resource Website
1+ mentions
Molecular Brain: Transcription Profiles of Mouse and Human Brains (RRID:SCR_008689) data or information resource, database MolecularBrain is an attempt to collect, collates, analyze and present the microarray derived gene expression data from various brain regions side by side. Transcription Profile of any gene in Mouse (online) and Human Brain (not yet) can be accessed as a histogram along with links to access various aspects of that gene. The expression levels were calculated from microarray data deposited at GEO (Gene expression omnibus). The molecular brain database could be searched using the built in search tool with the terms Entrez GeneID, gene symbol, synonym or description. Gene information along with their expression values can be also accessed from the alphabetical list of gene symbols on the footer. The protocol and GEO sample information is available. molecular, molecule, brain, transcription, mouse, human, gene, microarray, data, expression, database, tool, expression, molecular neuroanatomy resource has parent organization: National Institutes of Health nif-0000-37035 SCR_008689 Molecular Brain 2026-02-14 02:06:43 3
BrainNavigator
 
Resource Report
Resource Website
1+ mentions
BrainNavigator (RRID:SCR_008289) BrainNavigator data or information resource, atlas THIS RESOURCE IS NO LONGER IN SERVICE, documented December 31, 2013. An interactive atlas and 3D brain software for research, structure analysis, and education, it offers six atlases representing four species: the mouse, rat, monkey and human. The stereotaxic coordinates atlases are available for all four species and the rodent models have additional chemoarchitectonic atlases. BrainNavigator helps locate specific areas of the brain, making visualizing and experimental planning in the brain easier. *Plan: Browse 6 Atlases, Visualize with 3D models, Search Literature, Analyze gene expression, Identify connections *Publish: Access reference tools, Use and print images for publication, Search literature *Propose: Use and print images for proposals, Search literature, Locate gene expression in 2D and 3D, Identify connections *Produce: Simulate injections, Customize new coordinates, virtually slice sections, overlay atlas maps on your own images, create personal atlas maps With BrainNavigator, you''ll gain 24/7 access to their powerful 3D brain interactive software tool that helps further research in the neurosciences. In addition, their vast library of widely respected and referenced brain publications will provide a plethora of information on the most current brain research available. As publisher of the gold standard in brain atlas publications authored by the team around the leading brain cartographers George Paxinos and Charles Watson, they are pleased to bring an advanced tool to today''s neuroscientists and educators. Combining atlas content and 3D capabilities based on technologies from the Allen Institute for Brain Science, this online workflow solution brings brain research, analysis and education tools to your fingertips. 3d, 2d, acetylcholinesterase, anatomy, brain, coronal, reconstruction, sagittal, sterotaxic, visualization, molecular neuroanatomy resource, training resource, connection, literature, gene expression, image THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-24037 SCR_008289 Brain Navigator 2026-02-14 02:06:13 5
Manually Labeled MRI Brain Scan Database
 
Resource Report
Resource Website
1+ mentions
Manually Labeled MRI Brain Scan Database (RRID:SCR_009604) data or information resource, database Collection of neuroanatomically labeled MRI brain scans, created by neuroanatomical experts. Regions of interest include the sub-cortical structures (thalamus, caudate, putamen, hippocampus, etc), along with ventricles, brain stem, cerebellum, and gray and white matter and sub-divided cortex into parcellation units that are defined by gyral and sulcal landmarks. collection, neuroanatomical, MRI, brain, scan, data, thalamus, caudate, putamen, hippocampus, ventricle, cerebellum, cortex is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Neuromorphometrics
works with: MRI Neuroanatomy Labeling Services
works with: MRI Neuroanatomy Labeling Services
NIMH R43 MH60507;
NIMH R44 MH60507;
NIMH R43 MH084358
Commercially available nlx_155805 http://www.nitrc.org/projects/manuallabels SCR_009604 2026-02-14 02:06:11 1
Functional Neurogenesis
 
Resource Report
Resource Website
1+ mentions
Functional Neurogenesis (RRID:SCR_008830) Functional Neurogenesis data or information resource, narrative resource, blog A blog focusing on the function of adult neurogenesis in the dentate gyrus of the hippocampus, including discussion of scientific research papers, methods and protocols, and other trends or observations about the field. adult, neurogenesis, dentate gyrus, hippocampus, brain, neuron, anxiety, depressive disorder, memory, plasticity nlx_144587 SCR_008830 Functional Neurogenesis - New neurons in the adult brain. How they work and what they are good for. 2026-02-14 02:06:15 2
Pediatric Imaging Neurocognition and Genetics
 
Resource Report
Resource Website
50+ mentions
Pediatric Imaging Neurocognition and Genetics (RRID:SCR_008953) PING data or information resource, database A large multi-site pediatric MRI and genetics data resource to facilitate studies of the genomic landscape of the developing human brain. It includes information about the developing mental and emotional functions of the children to understand the genetic basis of individual differences in brain structure and connectivity, cognition, and personality. Investigators on the project are studying 1400 children between the ages of 3 and 20 years so that links between genetic variation and developing patterns of brain connectivity can be examined. Investigators interested in the effects of a particular gene will be able to search the database for any brain areas or connections between areas that differ as a function of variation in a particular gene, and also to determine if the genes appear to affect the course of brain development at some point during childhood. A data exploration tool has been created for mapping and analyzing MRI data sets collected for PING and related developmental studies. Approved investigators will be able to view raw image sets and derived 3D brain maps of MRI and DTI data, conduct hypothesis testing, and graph brain area measures as they change across the time course of development. PING Cores * Coordinating Core: Functions include project management, screening of participants and maintaining the database * Neuroimaging Core: applying a standardized high-resolution structural MRI protocol involving 3-D T1-weighted scans, a T2-weighted volume, and a set of diffusion-weighted scans with multiple b values and diffusion directions, scans to estimate MRI relaxation rates, and gradient echo EPI scans for resting state fMRI. Importantly, adaptive motion compensation, using ����??PROMO����??, a novel real-time motion correction algorithm will be used. Specific PING protocols for each scanner manufacturer: ** PING MRI Protocol - GE ** PING MRI Protocol - Philips ** PING MRI Protocol - Siemens * Assessment Core: Cognitive assessments for the PING project are conducted using the NIH Toolbox for Cognition. * Genomics Core: functions as a central repository for receipt of saliva samples collected for each study participant. Once received, samples are catalogued, maintained, and DNA is extracted using state-of-the-field laboratory techniques. Ultimately, genome-wide genotyping is performed on the extracted DNA using the Illumina Human660W-Quad BeadChip. PING involves 10 sites throughout the country including UCSD, University of Hawaii, Scripps Genomics, UCLA, UC Davis, Kennedy Krieger Institute/Johns Hopkins, Sacker Institute/Cornell University, University of Massachusetts, Massachusetts General Hospital/Harvard, and Yale. Families who may want to participate in the study, or others who want to know more about it, may email questions to ping (at) ucsd.edu. pediatric, neuroimaging, genetics, child, early adult human, adolescent, genetic variant, magnetic resonance imaging, brain, gene, brain structure, connectivity, function, brain development, cognition, experimental protocol, saliva, dna, diffusion tensor imaging, image, genotype, dicom, imaging genomics, magnetic resonance, nifti, FASEB list is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: NIH Toolbox - Assessment of Neurological and Behavioral Function
has parent organization: University of California at San Diego; California; USA
has parent organization: Multimodal Imaging Laboratory
NIDA ;
ARRA ;
NICHD
Data Use Agreement required. nlx_151904 http://www.nitrc.org/projects/ping http://ping.chd.ucsd.edu/ SCR_008953 PING Study, Pediatric Imaging Neurocognition and Genetics (PING) 2026-02-14 02:06:36 76
Allen Mouse Brain Connectivity Atlas
 
Resource Report
Resource Website
100+ mentions
Allen Mouse Brain Connectivity Atlas (RRID:SCR_008848) ABA Mouse Connectivity data or information resource, atlas, spatially referenced dataset Map of neural connections in mouse brain, built on an array of transgenic mice genetically engineered to target specific cell types. In addition to the connectivity data, information about the transgenic mouse lines and genetic tracers is available. Consists of high resolution 2-D projectivity image data that can be viewed side-by-side with the associated reference atlas and other reference datasets. Enables 3-D visualization and spatial/ontological search of connectivity models through a combination of manual and informatics analyses. brain, connectivity, atlas, neural, projection, mutant, mouse, strain, image, histology, neuroimaging, data is used by: NIF Data Federation
is related to: Allen Mouse Brain Common Coordinate Framework
has parent organization: Allen Institute for Brain Science
has parent organization: Allen Brain Atlas
Allen Institute for Brain Science Free for academic use, Non-commercial, Acknowledgement required, Commercial use requires permission nlx_146253 http://connectivity.brain-map.org/static/brainexplorer SCR_008848 Allen Brain Atlas Connectivity Study, Allen Brain Mouse Connectivity, Allen Mouse Connectivity Atlas, Allen Brain Atlas Mouse Connectivity 2026-02-14 02:06:15 186
Multiple Sclerosis Research Australia Brain Bank
 
Resource Report
Resource Website
Multiple Sclerosis Research Australia Brain Bank (RRID:SCR_010747) MS Research Australia Brain Bank biomaterial supply resource, tissue bank, material resource Biomaterial supply resource which provides high quality and well-chracaterized brain tissue samples for MS research. Registered MS brain donors and their families are kept up to date on the latest progress in MS research. biomaterial supply resource, brain, brain tissue, brain bank, MS, multiple sclerosis is listed by: Multiple Sclerosis Discovery Forum Multiple Sclerosis Trish MS Research Foundation ;
University of Sydney ;
Collier Charitable Fund ;
NSW Government Office for Science and Medical Research ;
MS Research Australia
Free, Freely available SCR_013840, nlx_99028 SCR_010747 2026-02-14 02:06:39 0
LESYMAP
 
Resource Report
Resource Website
10+ mentions
LESYMAP (RRID:SCR_017967) software resource, software toolkit Software R package to conduct lesion-to-symptom mapping from human MRI data.Takes lesion maps and cognitive performance scores from patients with stroke, and maps brain areas responsible for cognitive deficit. Conduct, lesion, symptom, mapping, human, MRI, data, cognitive, performance, score, patient, brain, area, deficit Free, Available for download, Freely available https://dorianps.github.io/LESYMAP/ SCR_017967 Lesion to Symptom Mapping 2026-02-14 02:07:19 12
MGH Center for Morphometric Analysis
 
Resource Report
Resource Website
10+ mentions
MGH Center for Morphometric Analysis (RRID:SCR_000885) material resource, instrument supplier A center dedicated to developing and applying morphometric methods to biomedical imaging data such as high-resolution MRI. The lab uses automated and semi-automated software such that MRI brain images are segmented into anatomical regions of interest. Projects in both basic and applied brain research include research on strokes and tumors; medical image processing research includes shape analysis of anatomical brain regions and measurement and analysis of brain volumes. brain, neuroscience, imaging, mri, magnetic resonance imaging, morphometric, biomedical, software, automated, anatomy is listed by: Eagle I nlx_156387 http://harvard.eagle-i.net/i/0000012e-9721-d0fd-55da-381e80000000 SCR_000885 2026-02-14 02:07:26 15
Whole Brain Catalog Blog
 
Resource Report
Resource Website
Whole Brain Catalog Blog (RRID:SCR_000582) WBC Blog data or information resource, narrative resource, blog THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. The blog of the Whole Brain Catalog. crowdsourcing, mouse, brain, cell, neuron, simulation, microscopy, neuroscience, electron microscopy, light microscopy has parent organization: Whole Brain Catalog THIS RESOURCE IS NO LONGER IN SERVICE nlx_144534 SCR_000582 2026-02-14 02:07:17 0
NYU Institute for Pediatric Neuroscience Sample
 
Resource Report
Resource Website
NYU Institute for Pediatric Neuroscience Sample (RRID:SCR_010458) NYU IPN Sample, NYUIQ data or information resource, data set Datasets including a collection of scans from 49 psychiatrically evaluated neurotypical adults, ranging in age from 6 to 55 years old, with age, gender and intelligence quotient (IQ) information provided. Future releases will include more comprehensive phenotypic information, and child and adolescent datasets, as well as individuals from clinical populations. The following data are released for every participant: * At least one 6-minute resting state fMRI scan (R-fMRI) * * One high-resolution T1-weighted mprage, defaced to protect patient confidentiality * Two 64-direction diffusion tensor imaging scans * Demographic information (age, gender) and IQ-measures (Verbal, Performance, and Composite; Weschler Abbreviated Scale of Intelligence - WASI) * Most participants have 2 R-fMRI scans, collected less than 1 hour apart in the same scanning session. Rest_1 is always collected first. adult human, young human, intelligence quotient, child, adolescent, clinical, resting state fmri, t1-weighted, mprage, diffusion tensor imaging, fsiq, viq, piq, neuroimaging, brain, image collection has parent organization: 1000 Functional Connectomes Project
has parent organization: New York University; New York; USA
Neurotypical, Aging Autism Speaks ;
Stavros Niarchos Foundation ;
Leon Levy Foundation ;
Phyllis Green and Randolph Cwen ;
NIMH R01MH083246
Creative Commons Attribution-NonCommercial License nlx_157644 SCR_010458 NYU Phyllis Green and Randolph Cwen Institute for Pediatric Neuroscience Sample 2026-02-14 02:08:15 0
Virginia Tech Carilion Research Institute Sample
 
Resource Report
Resource Website
Virginia Tech Carilion Research Institute Sample (RRID:SCR_010459) VTCRI Sample data or information resource, data set Dataset including a T1 weighted anatomical image as well as two 10-minute resting state scans acquired during the same session from 25 psychiatrically screened healthy adults (community sample) ranging in age from 18 to 65 years old, with age, sex, education level, and ethnicity provided. Some subjects also returned several weeks after the first scan for a second scanning session. The number of days between scan sessions, for subjects that had two sessions, is indicated in the demographics spreadsheet. The study scanning protocol included: # 13 sec localizer # 4 minute 38 second T1 weighted anatomical # Subject given instructions for resting state scan #1 # 10 minute 4 second resting state scan #1 # Subject given instructions for resting state scan #2 # 10 minute 4 second resting state scan #2 Scanning was performed on one of three different 3T Siemens TIM TRIOs at the Human Neuroimaging Lab at Baylor College of Medicine in Houston, Texas. All scans were acquired using the standard Siemen''s TIM 12-channel head matrix. The resting state scans were acquired with a custom sequence that is a slight modification to the standard Siemen''s EPI sequence that supports real-time fMRI. Images were acquired slightly oblique to minimize dephasing in the orbito-frontal cortex. Detailed scanning parameters are included in separate .pdf files. resting state fmri, t1-weighted, mprage, adult human, early adult human, late adult human, middle adult human, image collection, neuroimaging, brain, demographic, fmri, aging has parent organization: 1000 Functional Connectomes Project
has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA
Healthy Creative Commons Attribution-NonCommercial License nlx_157645 SCR_010459 Virginia Tech CRI Sample 2026-02-14 02:07:42 0
Brain Maps
 
Resource Report
Resource Website
1+ mentions
Brain Maps (RRID:SCR_017314) data or information resource, atlas Atlas with global nervous system nomenclature ontology and flatmaps for structure of rat brain. Open access resource for neuroscience community. atlas, nervous, system, nomenclature, ontology, flatmap, structure, brain, rat PMID:29277900 Free, Freely available SCR_017314 Brain maps 4.0, Brain maps 2026-02-14 02:06:24 3
Brain Mysteries
 
Resource Report
Resource Website
Brain Mysteries (RRID:SCR_000504) data or information resource, narrative resource A blog featuring articles on the brain, consciousness, cognitive science, psychology and neurology. This resource is in Russian. research, blog, article, psychology, neurology, brain, consciousness, forum, cognitive, russian THIS RESOURCE IS NO LONGER IN SERVICE nlx_19443 SCR_000504 2026-02-14 02:06:37 0
Honey Bee Brain EST Project
 
Resource Report
Resource Website
1+ mentions
Honey Bee Brain EST Project (RRID:SCR_002389) Bee-ESTdb biomaterial supply resource, material resource A database integrating data from the bee brain EST sequencing project with data from sequencing and gene research projects from other organisms, primarily the fruit fly Drosophila melanogaster. The goal of Bee-ESTdb is to provide updated information on the genes of the honey bee, currently using annotation primarily from flies to suggest cellular roles, biological functions, and evolutionary relationships. The site allows searches by sequence ID, EST annotations, Gene Ontology terms, Contig ID and using BLAST. Very nice resource for those interested in comparative genomics of brain. A normalized unidirectional cDNA library was made in the laboratory of Prof. Bento Soares, University of Iowa. The library was subsequently subtracted. Over 20,000 cDNA clones were partially sequenced from the normalized and subtracted libraries at the Keck Center, resulting in 15,311 vector-trimmed, high-quality, sequences with an average read length of 494 bp. and average base-quality of 41. These sequences were assembled into 8966 putatively unique sequences, which were tested for similarity to sequences in the public databases with a variety of BLAST searches. The Clemson University Genomics Institute is the distributor of these public domain cDNA clones. For information on how to purchase an individual clone or the entire collection, please contact www.genome.clemson.edu/orders/ or generobi (at) life.uiuc.edu. expressed sequence tag, brain, behavior, cdna, blast, gene, annotation, microarray, gene expression, comparative genomics, cdna clone, resource:genbank is listed by: One Mind Biospecimen Bank Listing
is related to: One Mind Biospecimen Bank Listing
is related to: Gene Ontology
has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA
NSF ;
University of Illinois Critical Research Initiatives Program ;
Burroughs Wellcome Fund
PMID:11932240 Free nif-0000-00118 SCR_002389 Honeybee EST Project 2026-02-14 02:06:41 5
Advanced Neuroscience Imaging Research Laboratory Software Packages
 
Resource Report
Resource Website
10+ mentions
Advanced Neuroscience Imaging Research Laboratory Software Packages (RRID:SCR_002926) ANSIR Software software resource, software toolkit Research group based in the Department of Radiology of Wake Forest University School of Medicine devoted to the application of novel image analysis methods to research studies. The ANSIR lab also maintains a fully-automated functional and structural image processing pipeline supporting the image storage and analysis needs of a variety of scientists and imaging studies at Wake Forest. Software packages and toolkits are currently available for download from the ANSIR Laboratory, including: WFU Biological Parametric Mapping Toolbox, WFU_PickAtlas, and Adaptive Staircase Procedure for E-Prime. multimodal, image, analysis, biological, parametric, mapping, voxel, linear, model, regressor, software, matlab, visualization, statistical, inference, in vivo, brain imaging, brain has parent organization: Wake Forest School of Medicine; North Carolina; USA NIBIB R01EB004673;
NIBIB 1R03EB008670
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-30033 SCR_002926 Advanced Neuroscience Imaging Research Software, ANSIR Laboratory Software Packages 2026-02-14 02:06:56 37
Princeton University Confocal Microscopy Core Facility
 
Resource Report
Resource Website
Princeton University Confocal Microscopy Core Facility (RRID:SCR_017812) core facility, access service resource, service resource Core provides researchers with ability to visualize samples, from monolayers and small organisms, such as developing fly and fish embryos, to very thick sections from brain and other organ tissues by using instruments including laser point (LSCM) and field scanning confocal (CSU), Total Internal Reflectance Fluorescence (TIRF), Multi Photon (MP), and Widefield (WF). Services in imaging in mammalian cells, yeast cells, Drosophila and Zebrafish embryos and ovaries, bacteria, sections of brain and other tissues, in both fixed and live specimens, Quantitative imaging methods such as FRAP, FLIP, and FRET, software packages for image processing, analysis, and 3D image reconstruction. Confocal, microscopy, visualize, sample, fly, fish, embryo, thick, section, organ, tissue, brain, imaging, mammalian, cell, yeast, drosophila, zebrafish, ovary, bacteria, fixed, live, speciment, quantitative, 3D image, reconstruction, service, core, ABRF is listed by: ABRF CoreMarketplace ABRF_568 SCR_017812 Confocal Microscopy Core Facility 2026-02-14 02:08:11 0
Case Western Reserve University Imaging Research Core Facility
 
Resource Report
Resource Website
Case Western Reserve University Imaging Research Core Facility (RRID:SCR_017917) core facility, access service resource, service resource Core provides preclinical and clinical imaging instrumentation and techniques.Preclinical services include Bioluminescence,Fluorescence,In situ cryoimaging,Magnetic Resonance Imaging (MRI),Positron Emission Tomography (PET),Radiochemistry Synthesis, Scintigraphy,Ultrasound,X-ray / Computed Tomography (CT) / micro CT,Image Processing / Quantification clinical research imaging systems. Clinical services include Comprehensive MR imaging research services, Dedicated Siemens Skyra 3T MRI scanner, Large animal preclinical studies, or clinical human research may be conducted,Structural and functional brain scanning can be performed with Avotec LCD Projection System, Coodination of access to PET and CT scanners for additional preclinical and human imaging studies. Core includes PET radiopharmaceutical core facility. Core staff provide radiochemistry synthesis. Preclinical, clinical, imaging, instrumentation, technique, bioluminescence, fluorescence, in situ cryoimaging, magnetic, resonance, imagingi, MRI, positron, emission, tomography, radiochemistry, synthesis, scintigraphy, ultrasound, x-ray, CT, micro CT, image, processing, quantification, brain, scanning, service, core, ABRF is listed by: ABRF CoreMarketplace Open ABRF_797 SCR_017917 Imaging Research Core 2026-02-14 02:08:35 0
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 2026-02-14 02:05:03 26
MRIcron
 
Resource Report
Resource Website
1000+ mentions
MRIcron (RRID:SCR_002403) MRIcron data visualization software, software resource, data processing software, software application 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 2026-02-14 02:05:07 2194

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