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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Allen Human Reference Atlas, 3D, 2020 Resource Report Resource Website 1+ mentions |
Allen Human Reference Atlas, 3D, 2020 (RRID:SCR_017764) | reference atlas, data or information resource, atlas | Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas. | Parcellation, adult, human, brain, 3D, atlas, data |
is used by: BICCN has parent organization: Allen Institute works with: Developing Human Brain Atlas version 2 (DHBAv2) |
Allen Institute for Brain Science ; NIMH U01 MH114812 |
Free, Available for download, Freely available | SCR_017764 | 2026-08-03 09:36:44 | 3 | |||||||||
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Slingshot Resource Report Resource Website 50+ mentions |
Slingshot (RRID:SCR_017012) | software resource, software application, data processing software | Software R package for identifying and characterizing continuous developmental trajectories in single cell data. Cell lineage and pseudotime inference for single-cell transcriptomics. | identify, characterize, continuous, developmental, trajectory, single, cell, data, lineage, pseudotime, inference, transcriptomic | is used by: Totem | NIMH U01 MH105979; NIDCD R01 DC007235; NCRR S10 RR029668; Siebel Foundation ; NIA K01 AG045344; NHGRI T32 HG000047; California Institute of Regenerative Medicine |
PMID:29914354 | Free, Available for download, Freely available | SCR_017012 | 2026-08-03 09:36:42 | 84 | ||||||||
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JTK_CYCLE Resource Report Resource Website 1+ mentions |
JTK_CYCLE (RRID:SCR_017962) | software resource, software application, data processing software | Software R package for Detecting Rhythmic Components in Genome-Scale Data Sets. Non-parametric algorithm to identify rhythmic components in large datasets. Identifies and characterizes cycling variables in large datasets. | Washington University in St.Louis, detecting rhythmic, component, genome, scale, dataset, algorithm, non parametric, cycling, variable | NIMH P50 MH074924; NHBLI R01 HL097800; Pennsylvania Commonwealth Health Research Formula Funds |
PMID:20876817 | Free, Freely available | SCR_017962 | Jonckheere-Terpstra-Kendall-CYCLE | 2026-08-03 09:36:49 | 5 | ||||||||
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CloudReg Resource Report Resource Website |
CloudReg (RRID:SCR_022795) | image analysis software, software resource, software application, data processing software | Software automated, terascale, cloud based image analysis pipeline for preprocessing and cross modal, nonlinear registration between volumetric datasets with artifacts. Automatic terabyte scale cross modal brain volume registration. | brain volume, nonlinear registration, automatic terabyte scale, cross modal brain volume registration, image analysis pipeline, volumetric datasets with artifacts | is used by: BICCN | NIA R01 AG066184; NSF EEC 1707298; NIMH U19MH114821; Kavli Neuroscience Discovery Institute ; Karen Toffler Charitable Trust ; NIMH R01 MH099647; NIMH K08MH113039; NIDA 1K99DA050662; AP Giannini Foundation ; NINDS K99 NS116122; NIA P01AG009973; Johns Hopkins University Kavli Neuroscience Discovery Institute Postdoctoral Fellowship ; Microsoft Research |
PMID:34253927 | Free, Available for download, Freely available | https://github.com/neurodata/CloudReg/ | SCR_022795 | 2026-08-03 09:37:48 | 0 | |||||||
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University of Pittsburgh Conte Center for the Neuroscience of Mental Disorders Resource Report Resource Website |
University of Pittsburgh Conte Center for the Neuroscience of Mental Disorders (RRID:SCR_000014) | Pitt CCNMD, Conte Center | organization portal, data or information resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Conte Center for the Neuroscience of Mental Disorders (CCNMD) at the University of Pittsburgh offers a highly interactive scientific environment for the study of the neurobiology of schizophrenia. Integrates the laboratory and clinical research activities of investigators from the University of Pittsburgh Schools of Medicine and Arts and Sciences and the adjacent Carnegie Mellon University. | schizophrenia, gaba |
has parent organization: University of Pittsburgh; Pennsylvania; USA is parent organization of: University of Pittsburgh Brain Tissue Donation Program |
NIMH 5P50MH103204-03 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_144496 | SCR_000014 | Conte Center for the Neuroscience of Mental Disorders | 2026-08-03 09:30:56 | 0 | ||||||
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NeuroPedia Resource Report Resource Website 10+ mentions |
NeuroPedia (RRID:SCR_001551) | NeuroPedia | data or information resource, database | A neuropeptide encyclopedia of peptide sequences (including genomic and taxonomic information) and spectral libraries of identified MS/MS spectra of homolog neuropeptides from multiple species. | proteomics, peptide, neuropeptide, mass spectrometry assay, peptide sequence, spectrum, homolog | has parent organization: Center for Computational Mass Spectrometry | NCRR P41-RR024851; NIDA 5K01DA23065; NINDS R01 NS24553; NIDA R01 DA04271; NIMH R01 MH077305; NHLBI P01 HL58120 |
PMID:21821666 | Free, Freely available | nlx_152894 | SCR_001551 | NeuroPedia: Neuropeptide database and spectra library | 2026-08-03 09:31:26 | 12 | |||||
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EPMBA.ORG: Electronic Prenatal Mouse Brain Atlas Resource Report Resource Website 1+ mentions |
EPMBA.ORG: Electronic Prenatal Mouse Brain Atlas (RRID:SCR_001882) | EPMBA | data or information resource, atlas | The Electronic Prenatal Mouse Brain Atlas, EPMBA, at present consists of two sets of annotated images of coronal sections from Gestational Day (GD) 12 heads and GD 16 brains of C57BL/6J mice. Ten micron thick sections were stained with hematoxylin and eosin. Images were prepared at various resolutions for annotations and for high resolution presentation. A subset of sections were annotated and linked to anatomical terms. Additionally, horizontal sections of a GD 12 head were aligned and re-assembled into a 3D volume for digital sectioning in arbitrarily oblique planes. These images were captured using a Nikon E800 stereomicroscope with a 10X objective. The resolution is 1.35 pixels/micrometer. The PC program used to grab the images, Microbrightfield's Neurolucida (version 6), stitched together a mosaic of between 10 and 50 high-res images for each tissue slice, while the user focused the scope for each mosaic tile. Since the nature of optic lenses is to focus on one central point, it was difficult to obtain a uniformly-focused field of vision; as such, small areas of these images are blurred. Images were then transferred to a Macintosh and processed in Adobe Photoshop (version 7). Color levels were adjusted for maximum clarity of the tissue, and areas surrounding the tissue were cleared of artifacts. Each image is approximately 3350 pixels wide by 2650 pixels high. A scale bar with a length of 1350 pixels/mm is visible in the lower right-hand corner of each image. The annotations have been completed for the Atlas of Developing Mouse Brain Gestational (Embryonic) Day 12 (7/5/07) as well as the Atlas of Developing Mouse Brain Embryonic Day 16 (4/26/07). The 3D EPMBA data set has been mounted on a NeuroTerrain Atlas Server (NtAS). (6/27/07). | embryonic, brain, c57bl/6j, coronal, developing, developmental, gestational, head, horizontal sections, image, mouse, prenatal | has parent organization: East Tennessee State University; Tennessee; USA | Human Brain Project ; NIMH 263-MD-414639 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10452 | SCR_001882 | EPMBA.org, Electronic Prenatal Mouse Brain Atlas | 2026-08-03 09:31:37 | 1 | ||||||
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Human Brain Transcriptome Resource Report Resource Website 50+ mentions |
Human Brain Transcriptome (RRID:SCR_013742) | HBT | data or information resource, database | A data repository containing transcriptome and associated metadata for the developing and adult human brain. It provides genome-wide, exon-level transcriptome data from both sexes and multiple ethnicities. | human brain, transcriptome data, brain regions, FASEB list |
is related to: Spatio-temporal transcriptome of the human brain has parent organization: Yale University; Connecticut; USA |
NIMH U01MH081896 | PMID:19477152 | SCR_013742 | 2026-08-03 09:35:31 | 95 | ||||||||
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Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas Resource Report Resource Website 1+ mentions |
Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas (RRID:SCR_019267) | data or information resource, atlas | Website to visualize and share anatomical labels. Franklin and Paxinos (FP) based anatomical labels in Allen Common Coordinate Framework (CCF). Cell type specific transgenic mice and MRI atlas were used to adjust and further segment labels. New segmentations were created in dorsal striatum using cortico-striatal connectivity data. Anatomical labels were digitized based on Allen ontology, and web-interface was created for easy visualization. These labels provide resource to isolate and identify mouse brain anatomical structures. Open source data sharing will facilitate further refinement of anatomical labels and integration of data interpretation within single anatomical platform. | Anatomical labels, Allen Common Coordinate Framework, Franklin and Paxinos labels, MRI atlas, segment labels, transgenic mice, dorsal striatum, cortico-striatal connectivity data, mouse brain anatomical structure |
is used by: BICCN is related to: Allen Institute for Brain Science |
NIMH R01 MH116176; NINDS R01 NS10 8407; Pennsylvania Department of Health ; NIH Office of the Director R24 OD018559 |
PMID:31699990 | Free, Freely available | SCR_019267 | 2026-08-03 09:37:14 | 2 | ||||||||
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PIVOT software Resource Report Resource Website 10+ mentions |
PIVOT software (RRID:SCR_017210) | PIVOT | software resource, data processing software, software application, data analysis software | Software R package for interactive analysis and visualization of transcriptomics data. Operating systems are macOS, Linux, Windows. | Interactive, analysis, visualization, transcriptomics, data | is related to: University of Pennsylvania; Philadelphia; USA | NIMH U01 MH098953 | PMID:29304726 | Free, Available for download, Freely available | SCR_017210 | Platform for Interactive analysis and Visualization Of Transcriptomics, PIVOT, KimLabIDV | 2026-08-03 09:36:33 | 17 | ||||||
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Brain Image Library Resource Report Resource Website 10+ mentions |
Brain Image Library (RRID:SCR_017272) | BIL | service resource, data or information resource, data repository, storage service resource | Public, NIH-funded repository and analysis ecosystem for brain microscopy data, designed to store, share, and process massive volumetric datasets. It enables researchers to access whole-brain images, neuron morphologies, and spatial data without needing to download, fostering collaborative discovery. Used to deposit, analyze, mine, share and interact with large brain image datasets. | archive, dataset, confocal, microscopy, brain, image, data, brain microscopy data, |
is used by: BICCN is used by: BRAIN Initiative Cell Atlas Network is recommended by: National Library of Medicine is recommended by: BRAIN Initiative is listed by: DataCite is listed by: re3data.org is related to: BRAIN Initiative is related to: Allen Institute for Brain Science works with: CBI BrAinPI is organization facet of: BRAIN Initiative Cell Atlas Network |
BRAIN Initiative ; NIMH R24 MH114793 |
PMID:38187527 | Free, Available for download, Freely available | DOI:10.17616/R31NJN9G, DOI:10.35077, r3d100013956 | https://doi.org/10.17616/R31NJN9G, https://doi.org/10.17616/r31NJN9G, https://doi.org/10.35077/, https://dx.doi.org/10.35077/, https://doi.org/10.17616/R31NJN9G | SCR_017272 | Brain Image Library | 2026-08-03 09:36:34 | 16 | ||||
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Brain Observatory Storage Service and Database (BossDB) Resource Report Resource Website 10+ mentions |
Brain Observatory Storage Service and Database (BossDB) (RRID:SCR_017273) | BossDB, bossDB, BOSS DB | 3d spatial image, data repository, data or information resource, database, storage service resource, image, service resource | BossDB (Brain Observatory Storage Service and Database) is a cloud-based ecosystem for the storage and management of public large-scale volumetric neuroimaging and connectomics datasets. This includes volumetric Electron Microscopy and X-Ray Micro/Nanotomography data with support for multi-channel image data, segmentations, annotations, meshes, and connectomes. BossDB integrates with community resources for data access, processing, visualization, and analysis, and includes an API that enables metadata management, rendering, datatype conversions, and ingest. | Johns Hopkins University Applied Physics Laboratory, JHU/APL, database, electron microscopy, xray, data, storage, archive, BRAIN Initiative, EM, XRM, XNH, ecosystem |
is used by: BICCN is recommended by: National Library of Medicine is recommended by: BRAIN Initiative is related to: Scalable Analytics for Brain Exploration Research is related to: Ecosystem for Multi-modal Brain-behavior Experimentation and Research has parent organization: BRAIN Initiative has parent organization: Johns Hopkins University; Maryland; USA |
BRAIN Initiative ; NIMH R24 MH114785 |
DOI:10.1101/217745 | Open | https://github.com/jhuapl-boss/boss/ | SCR_017273 | Brain Observatory Storage Service, bossDB, Block and Object Storage Service, BOSSDB, Block and Object Storage Service Database, Brain Observatory Storage Service and Database, BossDB | 2026-08-03 09:37:01 | 27 | |||||
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Neuron Phenotype Ontology Resource Report Resource Website 1+ mentions |
Neuron Phenotype Ontology (RRID:SCR_017403) | NPO | controlled vocabulary, data or information resource, ontology | An ontology for describing the complex phenotypes of neurons. | Cell, type, phenotype, neuron, ontology |
is used by: BICCN is provided by: NIFSTD |
NIMH U24 MH114827; BRAIN Initiative |
Free, Freely available | SCR_017403 | 2026-08-03 09:36:51 | 2 | ||||||||
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gene Expression Analysis Resource Resource Report Resource Website 50+ mentions |
gene Expression Analysis Resource (RRID:SCR_017467) | gEAR | portal, production service resource, service resource, analysis service resource, data or information resource, software resource | Portal for visualization and analysis of multi omic data in public and private domains. Enables upload, visualization and analysis of scRNA-seq data. | Visualization, analysis, multi, omic, data, upload, scRNA-seq, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: University of Maryland School of Medicine; Maryland; USA |
NIMH MH114788; NIDCD R01 DC013817; NIMH R24 MH114815; Hearing Health Foundation (Hearing Restoration Project) |
Restricted | SCR_017467 | gene Expression Analysis Resource | 2026-08-03 09:37:03 | 76 | |||||||
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TReNA Resource Report Resource Website |
TReNA (RRID:SCR_017458) | network analysis software, software application, data processing software, data analysis software, software resource | Methods for reconstructing transcriptional regulatory networks. | Reconstructing, transcriptional, regulatory, network, BRAIN Initiative | is recommended by: BRAIN Initiative | NIMH MH114788 | Free, Available for download, Freely available | SCR_017458 | 2026-08-03 09:36:38 | 0 | |||||||||
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ChromHMM Resource Report Resource Website 10+ mentions |
ChromHMM (RRID:SCR_018141) | software resource, data processing software, software application, data analysis software | Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. | Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern |
is listed by: Debian is listed by: OMICtools |
NHGRI U54 HG004570; NHGRI RC1HG005334; NIEHS R01 ES024995; NHGRI U01 HG007912; NIMH U01 MH105578; NSF 0905968; Alfred P. Sloan Fellowship ; CAREER Award |
PMID:29120462 PMID:22373907 |
Free, Available for download, Freely available | OMICS_03490 | https://sources.debian.org/src/chromhmm/ | SCR_018141 | 2026-08-03 09:37:12 | 47 | ||||||
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HIV Brain Sequence Database Resource Report Resource Website 1+ mentions |
HIV Brain Sequence Database (RRID:SCR_008819) | HIVBrainSeqDB | data or information resource, database | The HIV Brain Sequence Database (HIVBrainSeqDB) is a public database of HIV envelope sequences, directly sequenced from brain and other tissues from the same patients. For inclusion in the database, sequences must: (i) be deposited in Genbank; (ii) include some portion of the HIV env region; (iii) be clonal, amplified directly from tissue; and (iv) be sampled from the brain, or sampled from a patient for which the database already contains brain sequence. Sequences are annotated with clinical data including viral load, CD4 count, antiretroviral status, neurocognitive impairment, and neuropathological diagnosis, all curated from the original publication. Tissue source is coded using an anatomical ontology, the Foundational Model of Anatomy, to capture the maximum level of detail available, while maintaining ontological relationships between tissues and their subparts. 44 tissue types are represented within the database, grouped into 4 categories: (i) brain, brainstem, and spinal cord; (ii) meninges, choroid plexus, and CSF; (iii) blood and lymphoid; and (iv) other (bone marrow, colon, lung, liver, etc). Currently, the database contains 2517 envelope sequences from 90 patients, obtained from 22 published studies. 1272 sequences are from brain; the remaining 1245 are from blood, lymph node, spleen, bone marrow, colon, lung and other non-brain tissues. The database interface utilizes a faceted interface, allowing real-time combination of multiple search parameters to assemble a meta-dataset, which can be downloaded for further analysis. This online resource will greatly facilitate analysis of the genetic aspects of HIV macrophage tropism, HIV compartmentalization and evolution within the brain and other tissue reservoirs, and the relationship of these findings to HIV-associated neurological disorders and other clinical consequences of HIV infection. | human immunodeficiency virus, hiv, brain, sequence, hiv envelope sequence, brain sequence, clone, tissue, brainstem, spinal cord, meninges, choroid plexus, csf, blood, lymphoid, bone marrow, colon, lung, liver, aids |
is related to: FMA has parent organization: Harvard University; Cambridge; United States |
Human immunodeficiency virus | ARRA ; NIMH 3ROI MH83588-12S1; NIMH MH83588 |
PMID:21156070 | nlx_149217 | SCR_008819 | The HIV Brain Sequence Database | 2026-08-03 09:34:12 | 1 | |||||
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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 | 2026-08-03 09:34:08 | 1 | |||||||
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ABIDE Resource Report Resource Website 100+ mentions |
ABIDE (RRID:SCR_003612) | ABIDE | data or information resource, data set | Resting state functional magnetic resonance imaging (R-fMRI) datasets from 539 individuals with autism spectrum disorder (ASD) and 573 typical controls. This initiative involved 16 international sites, sharing 20 samples yielding 1112 datasets composed of both MRI data and an extensive array of phenotypic information common across nearly all sites. This effort is expected to facilitate discovery science and comparisons across samples. All datasets are anonymous, with no protected health information included. | phenotype, resting state functional magnetic resonance imaging, mri, image, fmri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: 1000 Functional Connectomes Project has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Autism spectrum disorder, Normal | Leon Levy Foundation ; Joseph P. Healy ; Stavros Niarchos Foundation ; NIMH K23MH087770; NIMH R03MH096321 |
Account required, Creative Commons Attribution-NonCommercial-ShareAlike License, v3 | nlx_157761 | SCR_003612 | Autism Brain Imaging Data Exchange | 2026-08-03 09:32:12 | 212 | |||||
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Limited Access Datasets From NIMH Clinical Trials Resource Report Resource Website 1+ mentions |
Limited Access Datasets From NIMH Clinical Trials (RRID:SCR_005614) | Limited Access Datasets From NIMH Clinical Trials | data or information resource, data set | A listing of data sets from NIMH-supported clinical trials. Limited Access Datasets are available from numerous NIMH studies. NIMH requires all investigators seeking access to data from NIMH-supported trials held by NIMH to execute and submit as their request the appropriate Data Use Certification pertaining to the trial. The datasets distributed by NIMH are referred to as limited access datasets because access is limited to qualified researchers who complete Data Use Certifications. | clinical trial, mental health, child |
uses: ClinicalTrials.gov uses: Sequenced Treatment Alternatives to Relieve Depression Study uses: CATIE - Clinical Antipsychotic Trials in Intervention Effectiveness uses: CATIE - Alzheimers Disease uses: Systematic Treatment Enhancement Program for Bipolar Disorder (STEP-BD) uses: TADS - Treatment for Adolescents with Depression Study uses: Treatment of SSRI-resistant Depression in Adolescents (TORDIA) is listed by: re3data.org has parent organization: NIMH Clinical Trials |
Depressive Disorder, Attention deficit-hyperactivity disorder, Autism Spectrum Disorder, Bipolar Disorder, Alzheimer's disease, Anxiety, Schizophrenia, Pervasive Development Disorder | NIMH | Approval required, Data Use Certification required | nlx_146232 | http://www.nimh.nih.gov/funding/clinical-trials-for-researchers/datasets/ | http://www.nimh.nih.gov/trials/datasets/nimh-procedures-for-requesting-data-sets.shtml, http://www.nimh.nih.gov/health/trials/datasets/ | SCR_005614 | Available Limited Access Datasets From NIMH Clinical Trials | 2026-08-03 09:32:44 | 1 |
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