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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MonkeyCBP Resource Report Resource Website 1+ mentions |
MonkeyCBP (RRID:SCR_017640) | MonkeyCBP | algorithm resource, software resource, software toolkit | Software toolbox for connectivity based parcellation of monkey brain. Integrated pipeline realizing tractography based brain parcellation with automatic processing and massive parallel computing. Highly automated process and high throughput performance supported by GPU option makes toolbox ready to be used by research community. | MonkeyCBP, Atlas, Parcellation Atlas, neuroimaging pipeline, brain, | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Freely available | SCR_017675 | http://www.nitrc.org/projects/monkey-cbp/ | SCR_017640 | Monkey Connectivity Based Parcellation; MonkeyCBP: A toolbox for connectivity-based parcellation of monkey brain | 2026-09-12 12:58:55 | 2 | ||||||
|
Knowing what you know (kwyk) - Bayesian Brain Parcellation Resource Report Resource Website |
Knowing what you know (kwyk) - Bayesian Brain Parcellation (RRID:SCR_017470) | kwyk | data processing software, image analysis software, segmentation software, software application, software resource | Software tool as deep neural network for predicting FreeSurfer segmentations of structural MRI volumes. This tool is implemented as both Docker and Singularity containers. Used for brain parcellation and uncertainty estimation. | Deep, neural, network, prediction, FreeSurfer, segmentation, structural, MRI, volume, brain, parcellation, uncertainty, estimation | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | https://github.com/neuronets/kwyk | SCR_017470 | knowing what you know | 2026-09-12 12:58:53 | 0 | |||||||
|
BrainMaker Resource Report Resource Website 1+ mentions |
BrainMaker (RRID:SCR_017666) | 3d visualization software, data processing software, data visualization software, image analysis software, image reconstruction software, software application, software resource | Software tool to automatically align sections to visualize brains in 3D. Assists with cell mapping, cytoarchitectonics and other areas requiring characterization of neuronal circuitry to create comprehensive anatomical reference. Automatically creates full resolution, 3D reconstructions of entire brain or any organ from serial sections of whole slide images. Allows to view cells, structures, and lesions, locate neurons expressing particular gene or visualize axonal projections of specific neurons with full anatomical context. | BMF Bioscience, align, section, visualize, brain, 3D, cell, mapping, cytoarchitectonics, neural, circuitry, anatomical, reference, brain, organ, serial, slide, image | Restricted | SCR_017666 | 2026-09-12 12:58:55 | 1 | |||||||||||
|
Colour maps for brain imaging Resource Report Resource Website 1+ mentions |
Colour maps for brain imaging (RRID:SCR_016715) | data processing software, data visualization software, image analysis software, software application, software resource | Software tool as a perceptually uniform color maps. Used in scientific literature to reflect data of brain imaging. | perceptually, uniform, color, map, brain, data, imaging |
is related to: MRIcron is related to: MATLAB has parent organization: University of Western Australia; Perth; Australia |
Free, Available for download, Freely available | SCR_016715 | Colour maps, brain_colours, colour maps, brain colours, Brain colours, colour maps for brain imaging, Colour maps for brain imaging | 2026-09-12 12:58:43 | 1 | |||||||||
|
ANOCVA Resource Report Resource Website |
ANOCVA (RRID:SCR_016719) | ANOCVA | data analysis software, data processing software, software application, software resource | Software R package as a nonparametric statistical test to compare clustering structures with applications in functional magnetic resonance imaging data (fMRI). Used for analysis of cluster variability in the diagnosis of neuropsychological disorders. | nonparametric, statistical, test, compare, clustering, structure, functional, brain, network, magnetic, resonance, imaging, data, fMRI, bio.tools |
is listed by: Debian is listed by: bio.tools is affiliated with: CRAN |
CAPES and CNPq Fellowships ; Ciência sem Fronteiras Fellowship ; NAP eScience ; Pew Latin American Fellowship ; State of São Paulo Research Foundation |
PMID:28174516 | Free, Available for download, Freely available | biotools:anocva | https://bio.tools/anocva | SCR_016719 | ANalysis Of Cluster VAriability, Analysis of Cluster Variability | 2026-09-12 12:58:43 | 0 | ||||
|
MouseLight Project Resource Report Resource Website 10+ mentions |
MouseLight Project (RRID:SCR_016668) | analysis service resource, data access protocol, data analysis service, data or information resource, database, portal, production service resource, service resource, software resource, web service | Software imaging platform to generate datasets of whole mouse brains imaged at submicron resolution that allow reconstructions of complete axonal arbors of individual neurons across the entire mouse brain. | neuronal, reconstruction, connectomics, projectomics, brain, tissue, image, dataset, mouse, axonal, arbor, individual, neuron |
is related to: Allen Institute for Brain Science has parent organization: Janelia Research provides: MouseLight Neuron Browser |
Free, Freely available, Tutorial available, Acknowledgement required, Registration required | http://mouselight.janelia.org/ | SCR_016668 | MouseLight, The Mouse Light Project, Janelia MouseLight project, Mouse Light Project, Mouse Light, MouseLight Project | 2026-09-12 12:58:43 | 12 | ||||||||
|
rsfMRI_fconn calculation Resource Report Resource Website 1+ mentions |
rsfMRI_fconn calculation (RRID:SCR_016591) | rsfMRI_fconn calculation | data analysis software, data processing software, software application, software resource | Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity. | data, resting, state, brain, processing, functional, magnetic, resonance, imaging, measurement, calculate, region, connectivity, analysis, sequence |
uses: SPM is related to: MATLAB |
SCR_016591 | resting state functional MRI and functional connectivity calculation, resting state functional MRI pre processing and Functional Connectivity calculation | 2026-09-12 12:58:42 | 1 | |||||||||
|
AFIDs Resource Report Resource Website 1+ mentions |
AFIDs (RRID:SCR_016623) | AFIDs | continuing medical education, data processing software, image processing software, software application, software resource, software toolkit, training resource | Open framework for evaluating correspondence between brain images and teaching neuroanatomy. | evaluate, correspondence, magnetic, images, human, brain, fiducial, placement, neuroanatomy | DOI:10.1002/hbm.24693 | Free, Available for download, Freely available | SCR_016623 | Anatomical Fiducials | 2026-09-12 12:58:42 | 3 | ||||||||
|
Allen Brain Atlas Resource Report Resource Website 100+ mentions |
Allen Brain Atlas (RRID:SCR_017001) | atlas, data or information resource, portal, project portal | Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases. | genomic, data, neuroanatomy, gene, expression, map, mouse, human, brain, atlas, neurobiology |
is related to: Allen Software Development Kit is related to: Common Cell Type Nomenclature has parent organization: Allen Institute has parent organization: Allen Institute for Brain Science is parent organization of: Allen Mouse Brain Reference Atlas is parent organization of: Allen Human Brain Atlas is parent organization of: Allen Developing Mouse Brain Atlas is parent organization of: Allen Mouse Brain Connectivity Atlas is parent organization of: Allen Mouse Spinal Cord Atlas is parent organization of: CellTax vignette is parent organization of: Allen Brain Atlas expression map of Cre and other drivers provides: ABA Mouse Brain: Atlas works with: Transcriptomics Explorer works with: Kinase Associated Neural Phospho Signaling |
Free, Freely available | SCR_017530 | SCR_017001 | Allen Brain Atlas, Brain Atlases, Allen Mouse Brain Atlas, The Allen Brain Atlas, Allen Human Brain Atlas | 2026-09-12 12:58:47 | 237 | ||||||||
|
Kinarm: End-Point Lab Resource Report Resource Website 1+ mentions |
Kinarm: End-Point Lab (RRID:SCR_017060) | instrument resource | Robotics research tool designed to make quantitative neurological assessments of sensorimotor, proprioception, and cognitive brain function by BKIN Technologies. Robotic manipulandum with display for studying arm movements. Allows to assess coordination of limbs at multiple joints while measuring joint specific force. | instrument, BKIN Technologies, kinarm, end, point, robot, quantitative, neurological, assessment, sensorimotor, proprioception, cognitive, limb, arm, brain, function | has parent organization: Queens University; Ontario; Canada | Commercially available | https://kinarm.com/wp-content/uploads/2023/03/Kinarm_Tech_End-Point-Lab_PN14332-1-Nov-21.pdf | https://www.bkintechnologies.com/bkin-products/kinarm-end-point-lab/ | SCR_017060 | KINARM End-Point Lab, Kinesiological Instrument for Normal and Altered Reaching Movements End-Point Lab | 2026-09-12 12:58:47 | 1 | |||||||
|
Data Archive BRAIN Initiative Resource Report Resource Website 10+ mentions |
Data Archive BRAIN Initiative (RRID:SCR_017114) | DABI | data or information resource, data repository, service resource, storage service resource | Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves. | shared, archive, human, invasive, neurophysiology, data, brain, neurotechnology, dataset, BRAIN Initiative |
is recommended by: National Library of Medicine is recommended by: BRAIN Initiative has parent organization: University of Southern California; Los Angeles; USA has parent organization: BRAIN Initiative |
BRAIN Initiative | Restricted | SCR_017114 | Data Archive Brain Initiative, DABI | 2026-09-12 12:58:48 | 17 | |||||||
|
MeshView Resource Report Resource Website 10+ mentions |
MeshView (RRID:SCR_017222) | data access protocol, software resource, web service | Web application for real time 3D display of surface mesh data representing structural parcellations and generation of user defined cut planes from volumetric atlases. | real, time, 3D, display, surface, mesh, data, structural, parcellation, generation, defined, cut, plane, volumetric, atlas, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: LocaliZoom is related to: Allen Institute for Brain Science has parent organization: University of Oslo; Oslo; Norway works with: Waxholm Space Atlas of the Sprague Dawley Rat Brain works with: Allen Mouse Brain Reference Atlas works with: Waxholm Space |
European Union Horizon 2020 Human brain project | DOI:10.1371/journal.pone.0216796 | Free, Freely available | https://localiview.apps.ebrains.eu/, https://meshview-for-brain-atlases.readthedocs.io, https://github.com/Neural-Systems-at-UIO/MeshView-for-Brain-Atlases | SCR_017222 | MeshView for brain atlases | 2026-09-12 12:58:50 | 11 | ||||||
|
Allen Software Development Kit Resource Report Resource Website 10+ mentions |
Allen Software Development Kit (RRID:SCR_018183) | AllenSDK | data analysis software, data processing software, software application, software resource | Software tool as code for processing and analyzing data in Allen Brain Atlas. Source code for reading and processing Allen Brain Atlas data. Allen SDK focuses on Allen Brain Observatory, Cell Types Database, and Mouse Brain Connectivity Atlas. | Data analysis, data processing, Allen Brain Atlas, data, brain |
is related to: Allen Brain Atlas is organization facet of: BICCN |
Free, Freely available | SCR_018192 | https://allensdk.readthedocs.io/en/latest/ | SCR_018183 | 2026-09-12 12:58:58 | 35 | |||||||
|
Gannet Resource Report Resource Website 100+ mentions |
Gannet (RRID:SCR_016049) | data analysis software, data processing software, software application, software resource, source code | Free, open-source MATLAB-based software toolkit for analyzing edited 1H magnetic resonance spectroscopy (MRS) data. | mri, magnetic resonance spectroscopy, mrs, batch, analysis, matlab, neuroscience, brain | PMID:25548816 | https://www.nitrc.org/projects/gannet/, https://markmikkelsen.github.io/Gannet-docs/index.html | http://www.gabamrs.com/about | SCR_016049 | Gannet - Batch Analysis of Edited Magnetic Resonance Spectroscopy (MRS) Data | 2026-09-12 12:58:34 | 167 | ||||||||
|
MRTool Resource Report Resource Website 10+ mentions |
MRTool (RRID:SCR_015956) | data or information resource, portal, topical portal | Software toolkit for analysis of MR brain imaging data. MRTool runs on Apple computers and PCs and requires SPM12. | brain, imaging, neuroimaging, analysis, magnetic, resonance, mr | requires: SPM | DOI:10.1007/s12021-018-9355-3 | Free, Available for download, Runs on MAC OS, Runs on Windows | SCR_015956 | 2026-09-12 12:58:32 | 14 | |||||||||
|
Marmoset Brain Connectivity Atlas Resource Report Resource Website 10+ mentions |
Marmoset Brain Connectivity Atlas (RRID:SCR_015964) | atlas, data or information resource, data repository, database, service resource, storage service resource | Brain connectivity atlas to create systematic, digital repository for data on connections between different cortical areas, in primate species. Data repository for connections between different cortical areas in marmoset monkeys. Allows access to data set and enables other interpretations of data, in light of future evolution of knowledge about marmoset cortex. | cortex, marmoset, monkey, cerebral, brain, architecture, primate |
has parent organization: Monash University; Melbourne; Australia has parent organization: Nencki Institute of Experimental Biology; Warsaw; Poland works with: Nencki-Monash template |
Australian Research Council CE140100007; Australian Research Council DP140101968; European Regional Development Fund ; International Neuroinformatics Coordinating Facility ; NIDA R01 DA036400; NIMH R01 MH087988 |
DOI:10.1038/s41467-020-14858-0 PMID:27099164 |
Free, Freely available | http://marmoset.braincircuits.org, http://analysis.marmosetbrain.org | SCR_015964 | Marmoset Monkey Cerebral Cortex Connectivity Atlas | 2026-09-12 12:58:33 | 26 | ||||||
|
NeuroXM Brain Science Suite Resource Report Resource Website |
NeuroXM Brain Science Suite (RRID:SCR_016372) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | Software toolkit for semantic integration of multi-modal brain data. It is used to collect, structure, connect, analyze and re-use brain data. | semantic, data, graph, neuroscience, neuroanatomy, ontology, circuitry, pathway, multimodal, brain | Commercially available | SCR_016372 | Brain Science Suite, NeuroXM, NeuroXM Suite | 2026-09-12 12:58:38 | 0 | ||||||||||
|
Neuroanatomy Atlas Resource Report Resource Website |
Neuroanatomy Atlas (RRID:SCR_002402) | Neuroanatomy Atlas | atlas, data or information resource | Annotated magnetic resonance brain images, both slices and surface views, normalized to Talairach space, along with annotations and a nice tutorial on image normalization. A viewer for MRI images (MRicro) is available and is described in a separate entry. Series of coronal, axial and sagittal brain slices along with some rendered volumes with major brain structures delineated. Slices are presented as static series with partial overlap of slices, so they are not suitable for 3d reconstruction. This neuroanatomy atlas shows regions on normalized MRI scans. Normalization is the process of warping a brain to match a standard size, orientation and shape of other brains. You can normalize MRI scans using programs like AIR, FLIRT or SPM. Once normalized, the overall shape of your MRI scan will approximately match those in this atlas. However, normalization preserves the unique sulcal features of each brain, so there will be some variation between your image and the images shown in this atlas. There is a great deal of individual variability even after normalization, so any atlas is only a rough guide to the shape and location of structures in an individuals brain. As I have noted before, secondary and tertiary sulci are not found in all individuals (Ono et al. 1990, Atlas of Cerebral Sulci). Another benefit of normalizing brains is it makes it easy to complete an accurate "scalp stripping" with brain extracting software (my MRIcro software implements Steve Smith's BET for this task). You can then create a useful volume rendering of the cortical surface. Typically, it is much easier to identify cortical sulci and gyri by looking at a rendered image of the brain's surface. This atlas shows you how to recognize these landmarks on a rendered MRI scan. | magnetic resonance imaging, neuroanatomy, brain | has parent organization: University of South Carolina; South Carolina; USA | Free, Available for download, Freely available | nif-0000-00121 | SCR_002402 | 2026-09-12 01:01:25 | 0 | ||||||||
|
Genes to Cognition Database Resource Report Resource Website |
Genes to Cognition Database (RRID:SCR_002735) | G2Cdb | data or information resource, database | Database of protein complexes, protocols, mouse lines, and other research products generated from the Genes to Cognition project, a project focused on understanding molecular complexes involved in synaptic transmission in the brain. | allele, gene list, mouse line, human disease, phenotyping, plasticity, behavior, proteonomics, brain, cognition, cognition disorder, learning, memory, neuroscience, experimental protocol, synapse proteomics, synapse | Wellcome Trust ; MRC ; BBSRC ; Gatsby Charitable Foundation ; Human Frontiers Science Programme ; European Union ; Framework Programme ; EPSRC ; NSF |
PMID:18984621 | Free, Freely available | nif-0000-02864 | http://www.genes2cognition.org/cgi-bin/SearchView | SCR_002735 | Genes-to-Cognition Database | 2026-09-12 01:01:26 | 0 | |||||
|
BAMS Cells Resource Report Resource Website 10+ mentions |
BAMS Cells (RRID:SCR_003531) | BAMS Cells, BAMS Cell | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023.BAMS is an online resource for information about neural circuitry. The BAMS Cell view focuses on the major brain regions and which cells are contained therein. | neuroanatomy, cell, neuron, neural circuitry, brain |
is used by: NIF Data Federation has parent organization: Brain Architecture Management System |
NIBIB ; NIMH ; NINDS |
THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-90175 | http://brancusi.usc.edu/bkms/ | SCR_003531 | Brain Architecture Management System Cells | 2026-09-12 01:01:29 | 11 |
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 dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET 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 dkNET then you can log in from here to get additional features in dkNET 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 dkNET 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.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
