Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Brain Research Institute Biobank Resources Resource Report Resource Website |
Brain Research Institute Biobank Resources (RRID:SCR_008756) | tissue bank, biomaterial supply resource, material resource, brain bank | Brain bank resources which include postmortem human frozen brain tissue and matched cerebrospinal fluid (CSF) and blood available for scientists to search for etiopathogeneses of human disease. The National Neurological Research Specimen Bank and the Multiple Sclerosis Human Neurospecimen Bank maintains a collection of quick frozen and formalin fixed postmortem human brain tissue and frozen cerebrospinal fluid from patients with neurological diseases, including Alzheimer's Disease, amyotrophic lateral sclerosis, depressive disorder/suicide, and epilepsy, among others. Diagnoses are documented by clinical medical records and gross/microscopic neuropathology. The Neuropathology Laboratory at the UCLA Medical Center maintains a bank of frozen, formalin and paraformaldehyde-fixed and paraffin-embedded postmortem human brain tissues and frozen cerebrospinal fluid (CSF) from patients who die with Alzheimer's disease and other dementing and degenerative illnesses, as well as control materials removed in a similar fashion from patients who are neurologically normal. | postmortem, brain, coronal, brain tissue, cerebral spinal fluid, blood, cerebral spinal fluid cell, cell-free cerebral spinal fluid, serum, plasma, buffy coat, frozen, formalin fixed, paraformaldehyde-fixed, paraffin-embedded, neurological disease, alzheimer's disease, amyotrophic lateral sclerosis, depressive disorder, suicide, epilepsy, huntington's disease, multiple sclerosis, parkinson's disease, progressive supranuclear palsy, schizophrenia, stroke, cerebrovascular accident, fronto-temporal dementia, neurologically normal, coronal section, control, clinical data |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Brain Research Institute |
Neurological disease, Alzheimer's disease, Amyotrophic Lateral Sclerosis, Depressive Disorder, Suicide, Epilepsy, Huntington's disease, Multiple Sclerosis, Parkinson's disease, Progressive Supranuclear Palsy, Schizophrenia, Stroke, Cerebrovascular Accident, Fronto-temporal dementia, Aging | NINDS ; NIMH ; National MS Society ; United States Department of Veterans Affairs ; Veterans Affairs West Los Angeles Healthcare Center ; NIA |
Public, Available to the research community | nlx_143996 | http://www.bri.ucla.edu/bri_research/research_resources.asp | SCR_008756 | Brain Research Institute Research Resources, Brain Research Institute Biobanks, BRI Research Resources, BRI Biobanks, BRI Biobank Resources | 2026-08-03 09:34:11 | 0 | |||||
|
Connectome Workbench Resource Report Resource Website 50+ mentions |
Connectome Workbench (RRID:SCR_008750) | CWB, wb_view, wb_command, wb_import | software toolkit, software resource, source code | Software brain visualization, analysis and discovery tool for fMRI and dMRI brain imaging data, including functional and structural connectivity data generated by the Human Connectome Project. Used to map brain imaging data. Allows for visualization of outputs from HCP pipelines from single subject, or average data from group of subjects and register that data onto standard brain atlas. | visualization, connectivity, brain, human, fMRI, dMRI, brain imaging data, map neuroimaging data, |
is used by: BRAIN Initiative Cell Atlas Network is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: FAIRsharing is related to: BALSA is related to: Washington University in St. Louis; Missouri; USA works with: ConnectomeDB works with: NIMP: Neuroanatomy-anchored Information Management Platform for Collaborative BICAN Data Generation |
NIH Blueprint for Neuroscience Research ; NIMH MH060974 |
Free, Available for download, Freely available | nlx_143924 | http://www.nitrc.org/projects/workbench, https://github.com/Washington-University/workbench, https://www.humanconnectome.org/software/workbench-command, https://www.humanconnectome.org/software/get-connectome-workbench, http://humanconnectome.org/connectome/connectome-workbench.html | SCR_008750 | 2026-08-03 09:34:08 | 56 | ||||||
|
Human Connectome Coordination Facility Resource Report Resource Website 500+ mentions |
Human Connectome Coordination Facility (RRID:SCR_008749) | WU-Minn HCP | image repository, service resource, data repository, storage service resource | Consortium to comprehensively map long-distance brain connections and their variability. It is acquiring data and developing analysis pipelines for several modalities of neuroimaging data plus behavioral and genetic data from healthy adults. | brain, connectivity, adult human, mri, resting-state fmri, functional mri assay, neuroimaging, surface rendering, time domain analysis, tractography, xnat pipeline |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL is related to: Brain Connectivity Toolbox is related to: FieldTrip is related to: BALSA has parent organization: Washington University in St. Louis; Missouri; USA has parent organization: NIH Human Connectome Project has parent organization: University of Minnesota Twin Cities; Minnesota; USA is parent organization of: WU-Minn HCP 500 Subjects MR and MEG Release |
healthy, twin | NIMH MH091657; NIH Blueprint for Neuroscience Research |
PMID:23684880 PMID:23702419 PMID:23668970 PMID:23702415 PMID:23702418 PMID:23707591 PMID:23702417 PMID:23684877 |
Free, Freely available | nlx_143922 | http://www.nitrc.org/projects/hcp_wuminn, http://www.humanconnectome.org/documentation/S500/ | SCR_008749 | HCP WU-Minn Consortium, WU-Minn: Human Connectome Project, HUMAN CONNECTOME PROJECT WU-Minn Consortium, WU-Minn Consortium: Human Connectome Project, WU-Minn Consortium: HCP | 2026-08-03 09:33:55 | 964 | |||
|
Neuroscience and Psychiatry Module 2: Fear/Safety Anxiety and Anxiety Disorders Resource Report Resource Website |
Neuroscience and Psychiatry Module 2: Fear/Safety Anxiety and Anxiety Disorders (RRID:SCR_008843) | Neuroscience and Psychiatry Module 2, Neuroscience Psychiatry Module 2 | narrative resource, video resource, data or information resource, training material | This is the second in a series of modules on neuroscience and psychiatry. This module describes neuroscience research on animal models of fear that informed human studies of fear/safety, anxiety and anxiety disorders. This model helps shed light on the symptoms of PTSD and lead to the development of a novel treatment that has been successful in research studies for several anxiety disorders. | neuroscience, psychiatry, fear, safety, anxiety, anxiety disorder, human, animal model, post-traumatic stress disorder, treatment |
is related to: Neuroscience and Psychiatry Module 1: Translating Neural Circuits into Novel Therapeutics has parent organization: NIMH Educational Resources |
NIMH | nlx_146229 | SCR_008843 | Neuroscience Psychiatry Module 2: Fear/Safety Anxiety Anxiety Disorders, Fear/Safety Anxiety and Anxiety Disorders | 2026-08-03 09:33:57 | 0 | |||||||
|
Treatment of SSRI-resistant Depression in Adolescents (TORDIA) Resource Report Resource Website |
Treatment of SSRI-resistant Depression in Adolescents (TORDIA) (RRID:SCR_008831) | TORDIA | portal, disease-related portal, clinical trial, topical portal, research forum portal, data or information resource | A multi-site, clinical research study examining treatment options for teens whose depression has not improved after one adequate trial of a selective serotonin reuptake inhibitor (SSRI), a type of antidepressant. The purpose of the study is to determine how best to treat adolescents with depression that is resistant to the first SSRI antidepressant they have tried. Participants receive one of three other antidepressant medications, either alone or in combination with cognitive behavioral therapy. The TORDIA study aims to develop useful clinical guidelines for the care and management of adolescent depression. Adolescents ages 12 to 18, currently taking a prescribed selective serotonin reuptake inhibitor (SSRI) and still experiencing depression, participate in a 12-week randomized treatment study that includes one of four conditions: (1) switching to an alternative SSRI, (2) switching to a different non-SSRI antidepressant, (3) switching to an alternative SSRI and receiving cognitive behavioral therapy (CBT), or (4) switching to a different non-SSRI antidepressant and receiving CBT. This is a double-blind study, which means that neither the participant nor the clinical staff will know which of the three possible medications has been assigned. Participants who respond to the assigned treatment will receive 12 additional weeks of the same treatment. Those who do not appear to be getting better will be offered 12 weeks of an alternative, individualized treatment plan based on each participant''s particular needs. All participants will receive follow-up psychiatric evaluations for 12 months after the 12-week continuation phase of the study, regardless of treatment adherence. For more information visit, http://www.clinicaltrials.gov/ct2/show/NCT00018902?term=clinical+trial+AND+treatment+of+ssri-resistant+AND+depression+AND+TORDIA+AND+study&rank=1 | young human, adolescent, depression, depressive disorder, clinical trial, selective serotonin reuptake inhibitor, antidepressant, nct00018902, drug, fluoxetine, venlafaxine, behavioral therapy, cognitive behavioral therapy, citalopram, treatment |
is used by: Limited Access Datasets From NIMH Clinical Trials has parent organization: ClinicalTrials.gov |
Depressive Disorder, Resistant to the first SSRI antidepressant | NIMH | PMID:20478877 | nlx_146237 | SCR_008831 | Treatment of SSRI-resistant Depression in Adolescents | 2026-08-03 09:34:13 | 0 | |||||
|
BMAP - Brain Molecular Anatomy Project Resource Report Resource Website 1+ mentions |
BMAP - Brain Molecular Anatomy Project (RRID:SCR_008852) | BMAP | funding resource, topical portal, data or information resource, portal | The Brain Molecular Anatomy Project is a trans-NIH project aimed at understanding gene expression and function in the nervous system. BMAP has two major scientific goals: # Gene discovery: to catalog of all the genes expressed in the nervous system, under both normal and abnormal conditions. # Gene expression analysis: to monitor gene expression patterns in the nervous system as a function of cell type, anatomical location, developmental stage, and physiological state, and thus gain insight into gene function. In pursuit of these goals, BMAP has launched several initiatives to provide resources and funding opportunities for the scientific community. These include several Requests for Applications and Requests for Proposals, descriptions of which can be found in this Web site. BMAP is also in the process of establishing physical and electronic resources for the community, including repositories of cDNA clones for nervous system genes, and databases of gene expression information for the nervous system. Most of the BMAP initiatives so far have focused on the mouse as a model species because of the ease of experimental and genetic manipulation of this organism, and because many models of human disease are available in the mouse. However, research in humans, other mammalian species, non-mammalian vertebrates, and invertebrates is also being funded through BMAP. For the convenience of interested investigators, we have established this Web site as a central information resource, focusing on major NIH-sponsored funding opportunities, initiatives, genomic resources available to the research community, courses and scientific meetings related to BMAP initiatives, and selected reports and publications. When appropriate, we will also post initiatives not directly sponsored by BMAP, but which are deemed relevant to its goals. Posting decisions are made by the Trans-NIH BMAP Committee |
has parent organization: National Institutes of Health is parent organization of: BMAP cDNA Resources |
Aging | NINDS ; NIMH ; NIDA ; NEI ; NIA ; NIAAA ; NICHD ; NIDCD ; NIEHS ; NHGRI ; NIGMS |
nlx_149083 | SCR_008852 | Brain Molecular Anatomy Project, Trans-NIH Brain Molecular Anatomy Project | 2026-08-03 09:34:09 | 6 | |||||||
|
NIMH Intramural Research Program Clinical Brain Disorders Branch Resource Report Resource Website 10+ mentions |
NIMH Intramural Research Program Clinical Brain Disorders Branch (RRID:SCR_008728) | CBDB | topical portal, data or information resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 07, 2013. A multidisciplinary neuroscience laboratory in which basic and clinical scientists work side by side exploring neural mechanisms and models of mental and cognitive function and of neuropsychiatric illness. Experiments are performed at many levels of inquiry, from basic molecular biology of the gene to clinical examinations of patients. A major area of investigation of this laboratory is the genetic mechanisms implicated in the pathogenesis of schizophrenia and its treatment. The laboratory is organized as a multi-disciplinary team of investigators with a common mission: to identify and fully characterize basic genetic and neurobiological mechanisms of schizophrenia and related cognitive and emotional disorders. The various components of this effort are centered various different units or divisions represented by groups of investigators, at various levels of training and experience, working on related experiments. The Director of the Branch and of the Genes, Cognition and Psychosis Program (GCAP) is Daniel R. Weinberger, M.D. The CBDB is the principle research laboratory in the created (2003) Genes, Cognition, and Psychosis Program (GCAP) of the NIMH. After twelve years of residing on the pastoral grounds of St. Elizabeths Hospital, in Southeast Washington, CBDB moved back to the main NIH campus in Bethesda, Maryland in 1998. While the unique setting of St. Elizabeths is irreplaceable, we have occupied beautiful new laboratories and clinic spaces that were created for us, and we are in the mainstream of NIH life., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | mental function, cognitive function, gene, clinical, treatment, pathogen |
is related to: Genes Cognition and Psychosis Program has parent organization: NIMH Division of Intramural Research Programs is parent organization of: NIMH Brain Tissue Collection |
Schizophrenia, Neuropsychiatric illness, Cognitive disorder, Emotional disorder | NIMH | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_143685 | SCR_008728 | NIMH Clinical Brain Disorders Branch, Clinical Brain Disorders Branch | 2026-08-03 09:34:08 | 13 | |||||
|
ERPLAB Resource Report Resource Website 100+ mentions |
ERPLAB (RRID:SCR_009574) | ERPLAB | software resource, data processing software, software application, data analysis software | A set of open source, freely available Matlab routines for analyzing Event Related Potential (ERP) data. It is tightly integrated with the EEGLAB Toolbox. ERPLAB routines can be accessed from the Matlab command window and from Matlab scripts in addition to being accessed from the EEGLAB GUI. Consequently, ERPLAB provides the ease of learning of a GUI-based system but also provides the power and flexibility of a scripted system.The development of ERPLAB Toolbox is being coordinated by Steve Luck and Javier Lopez-Calderon at the UC-Davis Center for Mind & Brain, with financial support from NIMH. | anova, eeg, meg, electrocorticography, event related potential, time domain analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Bioelectromagnetism Matlab Toolbox has parent organization: University of California at Davis; California; USA |
NIMH | GNU General Public License | nlx_155754 | http://www.nitrc.org/projects/erplab | SCR_009574 | ERPLAB Toolbox | 2026-08-03 09:34:13 | 428 | |||||
|
BRAINSDemonWarp Resource Report Resource Website 1+ mentions |
BRAINSDemonWarp (RRID:SCR_009524) | BRAINSDemonWarp | software application, data processing software, image analysis software, software resource, registration software | A command line program for image registration by using different methods including Thirion and diffeomorphic demons algorithms. The function takes in a template image and a target image along with other optional parameters and registers the template image onto the target image. The resultant deformation fields and metric values can be written to a file. The program uses the Insight Toolkit (www.ITK.org) for all the computations, and can operate on any of the image types supported by that library. This a an ITK based implementation of various forms of Thirion Demons based registration (including diffeomorphic demons registration originating from Tom Vercauteren at INRIA ). | magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center has parent organization: University of Iowa; Iowa; USA |
NINDS NS050568; NINDS NS40068; NIMH MH31593; NIMH MH40856 |
nlx_155700 | http://www.nitrc.org/projects/brainsdemonwarp | SCR_009524 | 2026-08-03 09:34:23 | 1 | |||||||
|
CrossExpression Resource Report Resource Website |
CrossExpression (RRID:SCR_027990) | software toolkit, software resource | Software package to discover genes that coordinate their expression across spatially adjacent cells. Used for analysis of spatial transcriptomic data allowing in-depth analyses how genes coordinate their expression in space to perform tissue-level functions. Facilitates analysis and exploration of cross-expression patterns. | analysis of spatial transcriptomic data, genes, coordinate genes expression in space, cross-expression patterns, | is organization facet of: BRAIN Initiative Cell Atlas Network | University of Toronto ; Ontario Graduate Scholarship ; NIMH R01MH133181; NIMH DP2MH132940; NIMH R01MH113005 |
PMID:41163012 | Free, Available for download, Freely available | SCR_027990 | 2026-08-02 09:09:44 | 0 | ||||||||
|
Factorial Mass Univariate Toolbox Resource Report Resource Website |
Factorial Mass Univariate Toolbox (RRID:SCR_028612) | software toolkit, software resource | Software toolbox (FMUT) is an extension to David Groppe’s Mass Univariate ERP Toolbox (MUT). MUT implements t-tests for several different mass univariate approaches to the analysis of ERP data. FMUT adds to this by implementing one-way and factorial ANOVA versions of the same mass univariate approaches. | NIMH R01 MH071635; NICHD R01 HD082527 |
PMID:31456213 | Free, Available for download, Freely available | https://github.com/ericcfields/FMUT | SCR_028612 | , Factorial Mass Univariate ERP Toolbox, Factorial Mass Univariate ERP Toolbox (FMUT) | 2026-08-02 09:09:47 | 0 | ||||||||
|
CommonMind Consortium Resource Report Resource Website 1+ mentions |
CommonMind Consortium (RRID:SCR_000139) | CommonMind | topical portal, data or information resource, portal | Sage Bionetworks, Mount Sinai School of Medicine (MSSM), University of Pennsylvania (Penn), the National Institute of Mental Health (NIMH), and Takeda Pharmaceuticals Company Limited (TAKEDA) have launched a Public-Private Pre-Competitive Consortium, the CommonMind Consortium, to generate and analyze large-scale genomic data from human subjects with neuropsychiatric disease and to make this data and the associated analytical results broadly available to the public. This collaboration brings together disease area expertise, large scale and well curated brain sample collections, and data management and analysis expertise from the respective institutions. As many as 450 million people worldwide are believed to be living with a mental or behavioral disorder: schizophrenia and bipolar disorder are two of the top six leading causes of years lived with disability according to the World Health Organization. The burden on the individual as well as on society is significant with estimates for the health care costs for these individuals as high as four percent GNP. This highlights a grave need for new therapies to alleviate this suffering. Researchers from MSSM including Dr. Pamela Sklar, Dr. Joseph Buxbaum and Dr. Eric Schadt will join with Dr. Raquel Gur and Dr. Chang-Gyu Hahn from Penn to combine their extensive brain bank collections for the generation of whole genome scale RNA and DNA sequence data. Dr.Pamela Sklar, Professor of Psychiatry and Neuroscience at MSSM commented this is an exciting opportunity for us to use the newest genomic methods to really expand our understanding of the molecular underpinnings of neuropsychiatric disease, while Dr Raquel Gur, Professor of Psychiatry from Penn observed this will be a great complement to some of the large-scale genetic analyses that have been carried out to date because it will give a more complete mechanistic picture. The CommonMind Consortium is committed to generating an open resource for the community and invites others with common goals to contact us at info (at) CommonMind.org. | molecular data, neuropsychiatric disease, human, data, brain bank, brain, dna, rna | has parent organization: Sage Bionetworks | Neuropsychiatric disease | Sage Bionetworks ; Mount Sinai School of Medicine; New York; USA ; University of Pennsylvania; Pennsylvania; USA ; Takeda ; NIMH |
nlx_144615 | http://commonmind.org/WP/ | SCR_000139 | 2026-08-03 09:30:58 | 4 | ||||||
|
LONI Visualization Tool Resource Report Resource Website |
LONI Visualization Tool (RRID:SCR_000765) | LONI Viz, LONI_Viz, LOVE | software resource, data visualization software, software application, data processing software | A versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. It reads Analyze, Raw-binary and NetCDF volumetric data, as well as, Multi-Contour Files (MCF), LWO/LWS surfaces, atlas hierarchical brain-region labelings ( Brain Trees). It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture. LONI_Viz allows the user to interactively overlay and browse through several data volumes, zoom in and out in the axial, sagittal and coronal views, and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest, e.g., sulcal curves, on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest. The 3D features of the package include a SurfaceViewer and a full real-time VolumeRenderer. These allow the user to view the relative positions of different anatomical or functional regions which are not co-planar in any of the axial, sagittal or coronal 2D projection planes. The interactive part of LONI_Viz features a region drawing module used for manual delineation of regions of interest. A series of 2D contours describing the boundary of a region in projection planes (axial, sagittal or coronal) could be used to reconstruct the surface-representation of the 3D outer shell of the region. The latter could then be resliced in directions complementary to the drawing-direction and these complementary contours could be loaded in all tree cardinal views. In addition the surface object could be displayed using the SurfaceViewer. A pre-loading data crop and sub-sampling module allows the user to load and view practically data of any size. This is especially important when viewing cryotome, histological or stained data-sets which may reach 1GB (109 bytes) in size. The user could overlay several pre-registered volumes, change intensity colors and ranges and the inter-volume opacities to visually inspect similarities and differences between the different subjects/modalities. Several image-processing aids provide histogram plotting, image-smoothing, etc. Specific Features: * Region description DataBase * Moleculo-genetic database * Brain anatomical data viewer * BrainMapper tool * Surface (LightWave objects/scenes) and Volume rendering tools * Interactive Contour Drawing tool Implementation Issues: * Applet vs. Application - the software is available as both an applet and a standalone application. The former could be used to browse data from within the LONI database, however, it imposes restrictions on file-size, Internet connection and network-bandwidth and client/server file access. The later requires a local install and configuration of the LONI_Viz software * Extendable object-oriented code (Java), computer architecture independent * Complete online software documentation is available at http://www.loni.ucla.edu/LONI_Viz and a Java-Class documentation is available at http://www.loni.ucla.edu/~dinov/LONI_Vis.dir/doc/LONI_Viz_Java_Docs.html | brain, atlas, visualization, gene mapping, atlas application, magnetic resonance, surface analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: Laboratory of Neuro Imaging |
Aging | NIA P50 AG16570; NLM 2R01 LM05639-06; NIA K08 AG100784; NCRR 2 P41 RR13642; NIMH 5 P01 MN52176; NSF DUE 0442992; NCRR U52 RR021813 |
PMID:16598642 | Free, Available for download, Freely available | nif-0000-23313 | http://www.nitrc.org/projects/incf_loni-viz | http://www.loni.ucla.edu/Software/LOVE | SCR_000765 | LONI Visualization Environment, LONI Viz environment, LOVE | 2026-08-03 09:31:08 | 0 | ||
|
NVM Resource Report Resource Website |
NVM (RRID:SCR_000600) | software resource, data visualization software, software application, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Software tool for quantitative neuroanatomical measurements in volumetric image data. Used to draw regions of interest for subsequent fMRI analysis. | quantitative, neuroanatomical, measurement, volumetric, image, data, draw, region, fMRI, analysis, morphology, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Neuromorphometrics |
NIMH R43 MH60507; NIMH R44 MH60507; NIMH R43 MH084358 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149080 | http://www.nitrc.org/projects/nvm | SCR_000600 | 2026-08-03 09:31:06 | 0 | |||||||
|
LONI Pipeline Processing Environment Resource Report Resource Website 10+ mentions |
LONI Pipeline Processing Environment (RRID:SCR_001161) | LONI Pipeline | workflow software, software resource, software application, data processing software | A free workflow application primarily aimed at neuroimaging researchers that allows users to easily describe their executables in a graphical user interface (ie. create a module) and connect them together to create complex analyses all without having to code a single line in a scripting language. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Once you����??ve created a module for use in the LONI Pipeline, you can save it into your personal library and reuse it in other workflows you create by simply dragging and dropping it in. Because the LONI Pipeline is written in Java, you can work in whatever operating system suits you best. If there are tools that you need that can only work on another operating system, you can install a Pipeline server on that computer and connect from your client to do processing and analysis remotely. | workflow, neuroscience, afni brik, analyze, bshort, bfloat, computational neuroscience, dicom, imaging genomics, java, linux, macos, microsoft, minc, minc2, nifti, pet, spect, posix/unix-like, sunos/solaris, windows, windows nt/2000, atlas, birn, ccb, functional, na-mic, registration, segmentation, statistical, surface analysis, visual processing environment, volume, warping, image processing |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at Los Angeles; California; USA |
NCRR P41 RR013642; NIMH R01 MH71940; NCRR U54 RR021813 |
PMID:12880830 | Free, Available for download, Freely available | nif-0000-00322 | http://www.nitrc.org/projects/pipeline | http://www.loni.ucla.edu/NCRR/Software/Pipeline.html | SCR_001161 | LONI Pipeline Environment | 2026-08-03 09:31:16 | 11 | |||
|
Mouse Brain Library Resource Report Resource Website 10+ mentions |
Mouse Brain Library (RRID:SCR_001112) | MBL | image collection, video resource, portal, database, topical portal, atlas, data or information resource | Collection of high resolution images and databases of brains from many genetically characterized strains of mice with aim to systematically map and characterize genes that modulate architecture of mammalian CNS. Includes detailed information on genomes of many strains of mice. Consists of images from approximately 800 brains and numerical data from just over 8000 mice. You can search MBL by strain, age, sex, body or brain weight. Images of slide collection are available at series of resolutions. Apple's QuickTime Plugin is required to view available MBL Movies. | brain, gene, genome, strain, c57bl/6j, dba/2j, a/j, genetic variant, phenotype, hippocampus, cerebellum, striatum, olfactory bulb, thalamus, neocortex, dorsal nucleus of lateral geniculate body, central nervous system |
is related to: Videoscribbler has parent organization: University of Tennessee Health Science Center; Tennessee; USA is parent organization of: MBL Pivot Collection is parent organization of: Mouse Brain Atlases |
NIMH P20 MH62009 | PMID:10857184 PMID:15043219 |
Restricted | nif-0000-00030 | SCR_001112 | MBL - Mouse Brain Library, Mouse Brain Library, The Mouse Brain Library | 2026-08-03 09:31:15 | 24 | |||||
|
Clarity resources Resource Report Resource Website 10+ mentions |
Clarity resources (RRID:SCR_001387) | CLARITY Resources | video resource, experimental protocol, narrative resource, data or information resource, training resource | Protocols and other training materials related to the CLARITY protocol, a technique for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. | workshop, protocol, specimen preparation, transparent brain, glass brain, brain, neuroimaging, phenotyping, tissue, brain tissue, cortex, hippocampus, thalamus, ventral, brainstem |
is used by: NIF Data Federation is used by: Integrated Videos has parent organization: Stanford University; Stanford; California |
NIMH 4R01MH099647-05 | PMID:23575631 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152559 | SCR_001387 | Clarity resource | 2026-08-03 09:31:18 | 18 | |||||
|
OBART Resource Report Resource Website 1+ mentions |
OBART (RRID:SCR_001903) | OBART | software resource, data or information resource, atlas, web application | Tool that provides an interactive method to examine quantitative relationships between brain regions defined by different digital atlases or parcellation methods. Its current focus is for human brain imaging, though the techniques generalize to other domains. The method offers a quantitative answer to the nomenclature problem in neuroscience by comparing brain parts on the basis of their geometrical definitions rather than on the basis of name alone. Thus far these tools have been used to quantitatively compare eight distinct parcellations of the International Consortium for Brain Mapping (ICBM) single-subject template brain, each created using existing atlasing methods. This resources provides measures of global and regional similarity, and offers visualization techniques that allow users to quickly identify the correspondences (or lack of correspondences) between regions defined by different atlases. | atlas, brain, clinical, mapping, meta-analysis, neuroscience, visualization, label |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Brain Architecture Project has parent organization: Boston University; Massachusetts; USA |
NIMH 5R01MH084802 | PMID:19787067 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10473 | http://www.nitrc.org/projects/obart | http://obart.brainarchitecture.org | SCR_001903 | The Online Brain Atlas Reconciliation Tool, Online Brain Atlas Reconciliation Tool | 2026-08-03 09:31:29 | 2 | |||
|
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 | 2026-08-03 09:32:15 | 3 | |||||||
|
Neurophysiology Imaging Facility Resource Report Resource Website |
Neurophysiology Imaging Facility (RRID:SCR_004080) | NIF | service resource, access service resource, core facility | 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) | 2026-08-03 09:32:36 | 0 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
