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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Primate Data Exchange Resource Report Resource Website 10+ mentions |
Primate Data Exchange (RRID:SCR_016435) | PRIME-DE | consortium, data or information resource, database, organization portal, portal | Open resource for nonhuman primate imaging.Used for aggregation independently acquired non-human primate magnetic resonance imaging (MRI) datasets and openly sharing them via the International Neuroimaging Data-sharing Initiative (INDI).Consortium and data collection for the neuroimaging community to map the non-human primate connectome. Anatomical, functional, and diffusion MRI datasets openly shared via the International Neuroimaging Data sharing Initiative (INDI). | nonhuman, primate, neuroimaging, magnetic, resonance, imaging, dataset, share | is affiliated with: 1000 Functional Connectomes Project | Joseph P. Healy ; NIMH P50 MH109429; NIMH R01 MH111439; the BRAIN Initiative ; the Max Planck Society ; the Sylvio O. Conte Center “Neurobiology and Dynamics of Active Sensing” |
DOI:10.1016/j.neuron.2018.08.039 | Restricted | SCR_016621 | SCR_016435 | PRIME-DE:PRIMate Data Exchange | 2026-09-05 06:28:08 | 16 | |||||
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B-CALM Resource Report Resource Website 1+ mentions |
B-CALM (RRID:SCR_023884) | instrument resource, software resource | Open source system for behavioral control based on Arduino Mega microcontroller and MATLAB based graphical interface and analysis code. Behavior controller optimized and customized for associative learning and memory tasks. Provided software should be able to control many different types of hardware for different task configurations. | OpenBehavior, instrument, behavioral controller, associative learning and memory, | is listed by: OpenBehavior | NIAAA R01AA029661; NIMH R00MH118422; NIMH R01MH129582; Scott Alan Myers Endowed Professorship |
PMID:37464151 | Free, Available for download, Freely available | https://edspace.american.edu/openbehavior/project/b-calm/ | SCR_023884 | 2026-09-05 06:33:16 | 1 | |||||||
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MR-PRESSO Resource Report Resource Website 100+ mentions |
MR-PRESSO (RRID:SCR_023697) | software resource, software toolkit | Software R package for performing Mendelian randomization pleiotropy residual sum and outlier method.Used to identify horizontal pleiotropic outliers in multi instrument summary level MR testing. | Mendelian randomization, identify horizontal pleiotropic outliers, multi instrument summary level MR testing, | American Heart Association Cardiovascular Genome Phenome Discovery ; AstraZeneca ; Goldfinch Bio ; NHGRI 5U01 HG009088; NHLBI R01 HL139865; NIGMS R35 GM124836; NIMH 1R01 MH094469; NIMH 1R01 MH107649 |
PMID:29686387 | Free, Available for download, Freely available | SCR_023697 | Mendelian Randomization Pleiotropy RESidual Sum and Outlier | 2026-09-05 06:33:15 | 100 | ||||||||
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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 | 2026-09-05 06:33:24 | 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 | Neurophysiology Imaging Facility (NIF) | 2026-09-05 06:33:25 | 0 | |||||||
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NKI/Rockland Sample Resource Report Resource Website 10+ mentions |
NKI/Rockland Sample (RRID:SCR_009435) | data or information resource, data set | A phenotypically rich neuroimaging sample, consisting of data obtained from individuals between the ages of 4 and 85 years-old. All individuals included in the sample undergo semi-structured diagnostic psychiatric interviews, and complete a battery of psychiatric, cognitive and behavioral assessments in order to provide comprehensive phenotypic information for the purpose of exploring brain / behavior relationships. | image collection, young human, late adult human, neuroimaging, phenotype, fmri, dti, mprage, t2, psychiatric assessment, cognitive assessment, behavioral assessment, resting state fmri, dicom, nifti |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Rockland Download Link Script is related to: NKI-RS Multiband Imaging Test-Retest Pilot Dataset is related to: NKI-RS Enhanced Sample has parent organization: 1000 Functional Connectomes Project |
Aging | New York State Office of Mental Health and Research Foundation for Mental Hygiene ; NKI Center for Advanced Brain Imaging CABI ; the Brain Research Foundation Chicago ; the Stavros Niarchos Foundation ; NIMH P50 MH086385-S1 |
Creative Commons Attribution-NonCommercial License | nlx_155538 | http://www.nitrc.org/projects/dl_dataset | SCR_009435 | Nathan Kline Institute / Rockland Sample, NKI Rockland Sample, Nathan Kline Institute (NKI) / Rockland Sample | 2026-09-05 06:33:30 | 17 | |||||
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NKI-RS Multiband Imaging Test-Retest Pilot Dataset Resource Report Resource Website 1+ mentions |
NKI-RS Multiband Imaging Test-Retest Pilot Dataset (RRID:SCR_010460) | NKI-RS Multiband Test-Retest Pilot Dataset | data or information resource, data set | A test-retest dataset to assess the reliability of multiband resting state fMRI (R-fMRI) and diffusion tensor imaging (DTI) scans prior to launch of the Enhanced Nathan Kline Institute - Rockland Sample (NKI-RS). The dataset is primarily composed of individuals from the initial NKI-RS - for these individuals psychiatric assessment information is available and included (participants were not excluded due to history of illness. In addition to R-fMRI and DTI, they included: 1) simple visual checkerboard stimulation fMRI scans to allow for assessment of traditional fMRI data quality metrics (e.g., contrast-to-noise ratio), 2) breath holding data to enable assessment of regional differences in vascular responsiveness, and 3) eye movement calibration scans to enable the assessment of eye-movement related artifacts which may be particularly troublesome for multiband sequences since several slices are acquired simultaneously. | demographic, multiband imaging, resting state fmri, diffusion tensor imaging, breath hold scan, eye movement calibration scan, visual stimulation scan, brain development, maturation, young human, late adult human, child, adolescent, adult human, image collection, pediatric, geriatric, behavior, cognitive, phentoyping, neuroimaging, dicom, nifti, multiband echo planar imaging, multiband resting state fmri, multiband diffusion tensor imaging, psychiatric assessment |
is related to: NKI/Rockland Sample is related to: NKI-RS Enhanced Sample has parent organization: 1000 Functional Connectomes Project has parent organization: Nathan S. Kline Institute for Psychiatric Research; New York; USA |
Aging | New York State Office of Mental Health and Research Foundation for Mental Hygiene ; Child Mind Institute 1FDN2012-1; NIMH R01MH094639-01; NIMH R01MH081218; NIMH R01MH083246; NIMH R21MH084126 |
Creative Commons Attribution-NonCommercial License | nlx_157648 | SCR_010460 | Enhanced Nathan Kline Institute-Rockland Sample Multiband Imaging Test-Retest Pilot Dataset, Enhanced Nathan Kline Institute-Rockland Sample (NKI-RS) Multiband Imaging Test-Retest Pilot Dataset | 2026-09-05 06:33:43 | 5 | |||||
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NKI-RS Enhanced Sample Resource Report Resource Website 50+ mentions |
NKI-RS Enhanced Sample (RRID:SCR_010461) | Enhanced NKI-RS | data or information resource, data set | Dataset of 1000 characterized community-ascertained participants using state-of-the-art multiband imaging-based resting state fMRI (R-fMRI) and diffusion tensor imaging (DTI), genetics, and a deep phenotyping protocol from a large cross-sectional sample of brain development, maturation and aging (ages 6 - 85 yrs). The Center for Magnetic Resonance Research (CMRR), University of Minnesota, provided the NKI-RS effort with the latest version of the Multiband EPI sequence (Xu et al. 2012) and associated image reconstruction algorithms, enabling the acquisition of state-of-the-art imaging datasets for this large-scale imaging effort. The enhanced NKI-RS expands upon the phenotypic protocol of the original NKI-RS and captures a broad range of behavioral and cognitive phenomenology relevant to psychiatric health and illness. The validity and value of assessments were evaluated by consulting leaders in the field of psychiatric phenotyping. | demographic, multiband imaging, resting state fmri, diffusion tensor imaging, breath hold scan, eye movement calibration scan, visual stimulation scan, brain development, maturation, young human, late adult human, child, adolescent, adult human, image collection, pediatric, geriatric, behavior, cognitive, phentoyping, neuroimaging, dicom, nifti, multiband echo planar imaging, multiband resting state fmri, multiband diffusion tensor imaging, lifespan, physiological assessment, psychological assessment, genetic |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NKI/Rockland Sample is related to: NKI-RS Multiband Imaging Test-Retest Pilot Dataset is related to: Mind Research Network - COINS is related to: NIMH Repository and Genomics Resources has parent organization: Nathan S. Kline Institute for Psychiatric Research; New York; USA |
Aging | New York State Office of Mental Health and Research Foundation for Mental Hygiene ; Child Mind Institute 1FDN2012-1; NIMH R01MH094639-01; NIMH R01MH081218; NIMH R01MH083246; NIMH R21MH084126 |
Public, Data Usage Agreement | nlx_157649 | SCR_010461 | Enhanced Nathan Kline Institute - Rockland Sample | 2026-09-05 06:33:44 | 97 | |||||
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Eagle Resource Report Resource Website 50+ mentions |
Eagle (RRID:SCR_015991) | software resource, software toolkit | Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods. | hmm, hidden markov model, statistic, estimation, haplotype, phase, reference, panel, sequencing, algorithm, analysis, probability |
is listed by: Debian is listed by: OMICtools has parent organization: Broad Institute |
Austrian Science Fund J-3401; Dutch Brain Foundation ; Fannie and John Hertz Foundation ; NCRR S10 RR028832; NHGRI F32HG007805; NHGRI HG007022; NHGRI R01 HG006399; NHLBI HL117626; NIMH R01 MH101244; NWO 480-05-003; Wellcome Trust WT098051 |
PMID:27694958 PMID:27270109 |
Free, Available for download, Freely available | OMICS_14099, SCR_017262 | https://sources.debian.org/src/bio-eagle/, https://github.com/poruloh/Eagle, https://data.broadinstitute.org/alkesgroup/Eagle/downloads/ | SCR_015991 | Bio-eagle, Eagle1, Eagle2 | 2026-09-05 06:33:00 | 57 | |||||
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ALICE Resource Report Resource Website 1+ mentions |
ALICE (RRID:SCR_017463) | software resource, software toolkit | Software tool for automatic localization of intra-cranial electrodes for clinical and high density grids. Software for coregistering high density ECoG grids to MRI anatomy. | Localization, intra-cranial, electrode, clinical, high density, grid, coregistering, ECoG, MRI, BRAIN Initiative | is recommended by: BRAIN Initiative | BrainGain Smart Mix Programme ; Dutch Technology Foundation ; Netherlands Organization for Scientific Research ; NIMH MH111417 |
PMID:29100838 | Restricted | SCR_017463 | Automatic Localization of Intra-Cranial Electrodes | 2026-09-05 06:33:03 | 1 | |||||||
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Myriads Resource Report Resource Website 1+ mentions |
Myriads (RRID:SCR_017447) | data analytics software, software application, software resource | Software package for p value based multiple testing that also implements dependence test and p-value simulation. | P value, multiple, testing, simulation, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: bio.tools is listed by: Debian |
NIMH MH111416 | PMID:29186285 | biotools:myriads | https://bio.tools/myriads | SCR_017447 | SGoF+ | 2026-09-05 06:33:03 | 1 | ||||||
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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 | Multi modal Image Registration And Connectivity anaLysis | 2026-09-05 06:33:06 | 1 | ||||||
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Face Research Toolkit Resource Report Resource Website |
Face Research Toolkit (RRID:SCR_023322) | FaReT | software resource, software toolkit | Software toolkit of three dimensional models and software to study face perception. Collection of plugins used with MakeHuman to create face stimuli for experiments. | 3D, three dimensional models, study face perception, create face stimuli for experiments, | is related to: MakeHuman | NIMH R21MH112013 | PMID:32519291 | Free, Available for download, Freely available | SCR_023322 | 2026-09-05 06:33:14 | 0 | |||||||
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NGSCheckMate Resource Report Resource Website 1+ mentions |
NGSCheckMate (RRID:SCR_022994) | software resource, software toolkit | Software package for validating sample identity in next generation sequencing studies within and across data types. Used for identifying next generation sequencing data files from the same individual. Used for checking sample matching for NGS data. | Next Generation sequencing data file, identifying next generation sequencing data files, next generation sequencing, same individual data files, checking sample matching, NGS data. | Harvard Medical School Eleanor and Miles Shore Fellowship ; Korean Health Technology ; NEI R01EY024230; NIA K01AG051791; NIMH 1P50MH106933; NIMH 1U01MH106883; Randolph Hearst Fund |
PMID:28369524 | Free, Available for download, Freely available | SCR_022994 | 2026-09-05 06:33:12 | 8 | |||||||||
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PyMVPA Resource Report Resource Website 100+ mentions |
PyMVPA (RRID:SCR_006099) | PyMVPA | software application, software resource, software toolkit | A Python package intended to ease statistical learning analyses of large datasets. It offers an extensible framework with a high-level interface to a broad range of algorithms for classification, regression, feature selection, data import and export. While it is not limited to the neuroimaging domain, it is eminently suited for such datasets. PyMVPA is truly free software (in every respect) and additionally requires nothing but free-software to run. Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. This Python-based, cross-platform, open-source software toolbox software toolbox for the application of classifier-based analysis techniques to fMRI datasets makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine learning packages. | python, machine learning, fmri, eeg, neuroimaging, image analysis, scripting, multivariate pattern analysis, brain, meg, extracellular recording, algorithm, reusable library, analyze, c, console (text based), eeg, meg, electrocorticography, frequency domain, independent component analysis, linear, modeling, magnetic resonance, multivariate analysis, nifti, nonlinear, os independent, pet, spect, principal component analysis, python, regression, spatial transformation, statistical operation, temporal transformation, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: neurodebian is related to: CoSMoMVPA has parent organization: Dartmouth College; New Hampshire; USA has parent organization: Otto-von-Guericke University Magdeburg; Saxony-Anhalt; Germany |
German Academic Exchange Service PPP-USA D/05/504/7; NIMH MH080526; NSF SBE 0751008; James McDonnell Foundation 220020127 |
PMID:19184561 PMID:19212459 PMID:20582270 |
MIT License | nlx_151596 | http://www.nitrc.org/projects/pymvpa | SCR_006099 | Python MVPA, Multivariate Pattern Analysis in Python, PyMVPA - Multivariate Pattern Analysis in Python | 2026-09-05 06:32:37 | 144 | ||||
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NIMH Publications Resource Report Resource Website |
NIMH Publications (RRID:SCR_008846) | NIMH Publications | data or information resource, narrative resource | Publications put out by the National Institute of Mental Health. Publications are available by topic: Disorders: * Attention Deficit Hyperactivity Disorder (ADHD) * Anxiety Disorders * Autism * Bipolar Disorder * Borderline Personality Disorder * Depression * Eating Disorders * Generalized Anxiety Disorder * Obsessive-Compulsive Disorder (OCD) * Panic Disorder * Post-Traumatic Stress Disorder * Schizophrenia * Social Phobia Populations * Older Adults * Men''s Mental Health * Women''s Mental Health * Children and Adolescents Research * Basic Research * Clinical Research and Trials * Research Funding * Mental Health Services Research Other * Coping with Traumatic Events * Genetics * HIV/AIDS * Imaging * Medications * NIMH * Prevention * Statistics * Suicide Prevention * Treatments | spanish, mental health, mental disease, human, booklet, brochure, fact sheet | has parent organization: National Institute of Mental Health | NIMH | nlx_146238 | SCR_008846 | National Institute of Mental Health Publications | 2026-09-05 06:32:41 | 0 | |||||||
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Multimodal Surface Matching Resource Report Resource Website |
Multimodal Surface Matching (RRID:SCR_024929) | MSM | data processing software, image analysis software, registration software, software application, software resource | Software tool for registering cortical surfaces. Capable of driving alignment using wide variety of descriptors of brain architecture, function and connectivity. | registering cortical surfaces, brain architecture, function and connectivity, | is a plug in for: FSL | NIMH 1U54MH091657; NIMH F30 MH097312 |
PMID:24939340 | Free, Freely available | SCR_024929 | MSM:Multimodal Surface Matching | 2026-09-05 06:34:45 | 0 | ||||||
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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 | , Functional Magnetic Resonance Imaging of the Brain's Integrated Registration and Segmentation Tool | 2026-09-05 06:34:45 | 7 | ||||||
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WASP Resource Report Resource Website 1+ mentions |
WASP (RRID:SCR_025497) | software resource, software toolkit, source code | Software allele-specific pipeline for unbiased read mapping and molecular QTL discovery. Allele-specific software for robust molecular quantitative trait locus discovery. | molecular QTLs discovery, unbiased allele-specific read mapping and discovery, molecular QTLs, unbiased allele-specific read, mapping and discovery, | Howard Hughes Medical Institute ; NHGRI HG006123; NHGRI HG007036; NIGMS GM007197; NIMH MH101825; NSF |
PMID:26366987 | Free, Available for download, Freely available, | SCR_025497 | 2026-09-05 06:35:00 | 3 | |||||||||
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CellTax vignette Resource Report Resource Website 1+ mentions |
CellTax vignette (RRID:SCR_017000) | data or information resource, data set | Cellular Taxonomy of Mouse Visual Cortex by analyzing gene expression patterns at single cell level. Construction of cellular taxonomy of one cortical region, primary visual cortex, in adult mice done on basis of single cell RNA sequencing. | data, classification, cell, type, mammalian, brain, cellular, taxonomy, mouse, visual, cortex, gene, expression, pattern, cortical, region |
is related to: Allen Brain Atlas API is related to: Allen Mouse Brain Reference Atlas is related to: Allen Cell Types Database has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas |
Allen Institute for Brain Science ; NEI R01 EY023173; NIMH U01 MH105982 |
PMID:26727548 | Free, Public | SCR_017000 | Cellular Taxonomy of the Mouse Visual Cortex, Cellular Taxonomy of the Mouse Visual Cortex Allen Institue for Brain Science | 2026-09-05 06:34:10 | 3 |
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