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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
BioMesh3D Resource Report Resource Website 1+ mentions |
BioMesh3D (RRID:SCR_009534) | BioMesh3D | software application, software resource | A free, easy to use program for generating quality meshes for use in biological simulations. It is currently integrated with SCIRun and uses the SCIRun system to visualize the intermediate results. The BioMesh3D program uses a particle system to distribute nodes on the separating surfaces that separate the different materials and then uses the TetGen software package to generate a full tetrahedral mesh. | mesh, simulation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SCIRun is related to: SCIRun has parent organization: University of Utah; Utah; USA |
NCRR 5P41RR012553-15; NIGMS 8 P41 GM103545-15 |
PMID:23367171 | MIT License | nlx_155708 | http://www.nitrc.org/projects/biomesh3d | SCR_009534 | 2026-02-15 09:20:13 | 3 | |||||
|
BESA Resource Report Resource Website 100+ mentions |
BESA (RRID:SCR_009530) | BESA | software application, software resource | Software for source analysis and dipole localization in EEG and MEG research. BESA Research has been developed on the basis of 20 years experience in human brain research by Michael Scherg, University of Heidelberg, and Patrick Berg, University of Konstanz. BESA Research is a highly versatile and user-friendly Windows program with optimized tools and scripts to preprocess raw or averaged data for source analysis. All important aspects of source analysis are displayed in one window for immediate selection of a wide range of tools. BESA Research provides a variety of source analysis algorithms, a standardized realistic head model (FEM), and allows for fast and easy hypothesis testing and integration with MRI and fMRI. | application, connectivity analysis, eeg, meg, electrocorticography, eeg modeling, event related potential, finite element analysis, forward - inverse, fourier time-domain analysis, independent component analysis, meg modeling, modeling, principal component analysis, source separation analysis, spectral analysis, statistical operation, surrogate data analysis, temporal transformation, time domain analysis, evoked potential, evoked field, event-related field, neuroimaging, mri, fmri | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial license | nlx_155695 | http://www.nitrc.org/projects/besa | SCR_009530 | Brain Electrical Source Analysis | 2026-02-15 09:20:12 | 233 | ||||||
|
Hitachi2nirs Resource Report Resource Website |
Hitachi2nirs (RRID:SCR_009494) | Hitachi2nirs | software application, software resource | A Matlab script to convert the raw .csv Hitachi ETG4000 output file into a .nirs file for use with Homer2. The script also requires a .pos file. This is the output of the polhemus 3D digitiser that they use to record where the optodes are located spatially. I realize that not everyone uses a 3D digitiser so I have included three example .pos files - one for each of the possible optode arrangements of the Hitachi system (either two 3x3 arrays, one 3x5 array or one 4x4 array). If you use a different arrangement or have more probes than them, feel free to get in touch and they may be able to advise on how to create a model .pos file. There are two versions of the conversion script: 1. single - this will read in ONE .csv file and ONE .pos file and create ONE .nirs file 2. multi - this will read in a user-specified number of .csv files and ONE .pos file. It will then create one .nirs file for each .csv file that was read in and deposit it in the same directory as that .csv file. | hardware, matlab, nirs, fnir, optical imaging, optical imaging, physiological recording | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | BSD License | nlx_155642 | SCR_009494 | 2026-02-15 09:20:08 | 0 | ||||||||
|
ALVIN Resource Report Resource Website 1+ mentions |
ALVIN (RRID:SCR_009527) | ALVIN | software application, software resource | A fully automated algorithm which works within SPM8 to segment the lateral ventricles from structural MRI images. The algorithm has been validated in infants, adults and patients with Alzheimer's disease (ICC>0.95). ALVIN is insensitive to different scanner sequences (ICC>0.99, 8 different sequences 1.5T and 3T) and sensitive to changes in ventricular volume. Processing time is approx 10mins per subject. | magnetic resonance, quantification, region of interest, segmentation, software, volume measurement, volumetric analysis, volumetric analysis | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | GNU General Public License | nlx_155690 | http://www.nitrc.org/projects/alvin_lv | SCR_009527 | ALVIN - Automatic Lateral Ventricle delIneatioN, Automatic Lateral Ventricle delIneatioN, ALVIN - Lateral Ventricle Segmentation | 2026-02-15 09:20:09 | 6 | ||||||
|
fMRI-CPCA Resource Report Resource Website 1+ mentions |
fMRI-CPCA (RRID:SCR_009520) | fMRI-CPCA, fMRI CPCA | software application, software resource | Constrained Principal Component Analysis (CPCA) combines regression analysis and principal component analysis into a unified framework. This method derives images of functional neural networks from singular-value decomposition of BOLD signal time series, and allows derivation of images when the analyzed BOLD signal is constrained to the scans occurring in peristimulus time, using all other scans as baseline. CPCA provides allows (1) determination of multiple functional networks involved in a task, (2) estimation of the pattern of BOLD changes associated with each functional network over peristimulus time points, (3) quantification of the degree of interaction between these multiple functional networks, and (4) a statistical test of the degree to which experimental manipulations affect each functional network. fMRI CPCA provides all results in matlab.mat file format, as well as writing images in analyze format for all components, rotated and unrotated. | analyze, linux, macos, matlab, microsoft, magnetic resonance, nifti, posix/unix-like, principal component analysis, regression, statistical operation, windows | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | nlx_155682 | SCR_009520 | fMRI-Constrained Principal Component Analysis, fMRI Constrained Principal Component Analysis | 2026-02-15 09:19:45 | 7 | |||||||
|
GAMBIT Resource Report Resource Website 50+ mentions |
GAMBIT (RRID:SCR_009483) | GAMBIT | software application, software resource | An end-to-end application allowing Group-wise Automatic Mesh-Based analysis of cortIcal Thickness as well as other surface area measurements. This cross-platform tool can be run within 3D Slicer as an external module, or directly as a command line. | analyze, c++, linux, mesh generation, modeling, magnetic resonance, nrrd, posix/unix-like, surface analysis, thickness, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: 3D Slicer has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
BSD License | nlx_155631 | SCR_009483 | 2026-02-15 09:20:03 | 57 | ||||||||
|
GIMIAS Resource Report Resource Website 1+ mentions |
GIMIAS (RRID:SCR_009545) | GIMIAS | software application, software resource | A workflow-oriented environment focused on biomedical image computing and simulation. The open source framework is extensible through plug-ins and is focused on building research and clinical software prototypes. Gimias has been used to develop clinical prototypes in the fields of cardiac imaging and simulation, angiography imaging and simulation, and neurology. | analyze, c++, clinical neuroinformatics, dicom, microsoft, magnetic resonance, nifti, platform, posix/unix-like, software, win32 (ms windows), windows, computing, simulation, visualization, processing, clinical |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Pompeu Fabra University; Barcelona; Spain |
BSD License | nlx_155762 | http://www.nitrc.org/projects/gimias_fw | http://www.gimias.net/ | SCR_009545 | Graphical Interface for Medical Image Analysis and Simulation | 2026-02-15 09:19:45 | 6 | |||||
|
Neurodocker Resource Report Resource Website 1+ mentions |
Neurodocker (RRID:SCR_017426) | software application, software resource | Software tool to generate Dockerfiles and Singularity recipes for neuroimaging with simple command-line interface. Command line program that generates custom Dockerfiles and Singularity recipes for neuroimaging and minifies existing containers. Supports AFNI, ANTs, Convert3D, Dcm2niix, FreeSurfer, FSL, Matlab Compiler Runtime, MINC, Miniconda, MRtrix3, NeuroDebian, PETPVC, and SPM12. | Generate, Dockerfile, singularity, recipe, neuroimaging, command-line, interface, minify, container | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Freely available | https://www.nitrc.org/projects/neurodocker/ | SCR_017426 | 2026-02-15 09:22:05 | 4 | |||||||||
|
DW-MRI Random Walk Simulator Resource Report Resource Website |
DW-MRI Random Walk Simulator (RRID:SCR_006652) | DW-MRI Random Walk Simulator | software application, software resource, simulation software | A simple interface to simulate Brownian motion in arbitrary, complex environments. The analysis routines enable visualization of these models with DTI, q-space, and higher order diffusion weighted MRI. | java, macos, matlab, microsoft, modeling, monte carlo, magnetic resonance, posix/unix-like, random walk, simulation, dti, q-space, diffusion weighted mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: INCF Software Center |
GNU Lesser General Public License | nlx_155873 | http://www.nitrc.org/projects/randomwalks | SCR_006652 | 2026-02-16 09:46:46 | 0 | |||||||
|
Monte Carlo eXtreme Resource Report Resource Website 1+ mentions |
Monte Carlo eXtreme (RRID:SCR_007001) | MCX | software application, software resource, simulation software | A Monte Carlo simulation software for photon migration in 3D turbid media. It uses Graphics Processing Units (GPU) based massively parallel computing techniques and is extremely fast compared to the traditional single-threaded CPU-based simulations. Using an nVidia 8800GT graphics card (14MP/114Cores), the acceleration is about 300x~400x compared to a single core of Xeon 5120 CPU; this ratio can be as high as 700x with a GTX 280 GPU and 1400x with a GTX 470. | c, console (text based), macos, microsoft, modeling, monte carlo, optical imaging, other programming language, posix/unix-like, win32 (ms windows), windows |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: SourceForge |
GNU General Public License | nlx_155817 | http://www.nitrc.org/projects/mcextreme | SCR_007001 | Monte Carlo eXtreme (MCX) | 2026-02-16 09:46:51 | 2 | ||||||
|
Function BIRN Resource Report Resource Website 1+ mentions |
Function BIRN (RRID:SCR_007291) | FBIRN | data or information resource, topical portal, portal | The FBIRN Federated Informatics Research Environment (FIRE) includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection, storage, sharing and management, tracking, and analysis of large fMRI datasets. fBIRN is a national initiative to advance biomedical research through data sharing and online collaboration. BIRN provides data-sharing infrastructure, software tools, strategies and advisory services - all from a single source. | fmri, 3d model, data storage, imaging, map, morphology, mri, neuroinformatics, segmentation, software, talairach, volume, warping, analyze, application, c++, csh/tcsh, data, database, database application, data resource, dicom, javascript, linux, magnetic resonance, nifti, ontology, pl/sql, posix/unix-like, python, quality metrics, spatial transformation, statistical operation, tcl/tk, unix shell, visualization, web resource, web service, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Biomedical Informatics Research Network is parent organization of: BXH/XCEDE Tools is parent organization of: FBIRN Image Processing Scripts |
NIGMS ; NCRR 1U24-RR025736; NCRR U24-RR021992; NCRR U24-RR021760; NCRR 1U24-RR026057-01 |
nif-0000-00070 | http://www.nitrc.org/projects/fbirn | http://nbirn.net/tools/browse_tools.shtm | SCR_007291 | Functional Imaging BIRN | 2026-02-16 09:46:56 | 2 | |||||
|
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 | 2026-02-16 09:49:17 | 1 | ||||||
|
Penn Hippocampus Atlas Resource Report Resource Website 1+ mentions |
Penn Hippocampus Atlas (RRID:SCR_000421) | Penn Hippocampus Atlas | data or information resource, atlas | Atlas of segmented and normalized high-resolution postmortem MRI of the human hippocampus. Additional data (raw images) is available through the SCM link. It requires knowing how to use CVS. | magnetic resonance, nifti, hippocampus, mri, postmortem |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Pennsylvania; Philadelphia; USA |
NIA AG027785; NINDS NS061111; NINDS NS058386; NINDS NS045839 |
PMID:18840532 | Free, Available for download, Freely available | nlx_155920 | SCR_000421 | 2026-02-16 09:45:15 | 2 | ||||||
|
Licensing issues in software and data Resource Report Resource Website |
Licensing issues in software and data (RRID:SCR_000411) | NITRC Licensing | data or information resource, narrative resource, discussion | Discussion forum on licensing issues in software and data. All are invited to participate or join the project and contribute. A listing of software licenses are available. | license |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Free, Available for download, Freely available | nlx_155651 | SCR_000411 | 2026-02-16 09:45:15 | 0 | ||||||||
|
Kymata Atlas Resource Report Resource Website 1+ mentions |
Kymata Atlas (RRID:SCR_000269) | data or information resource, atlas | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An online atlas of neural function, maintained by Cambridge University and the MRC Cognition and Brain Sciences Unit (CBSU). | data visualization software, database, adult human, brain, function, computational model, sensory information, post-synaptic dendritic current |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Cambridge; Cambridge; United Kingdom has parent organization: MRC Cognition and Brain Sciences Unit |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_158115 | http://www.nitrc.org/projects/kymata_atlas | SCR_000269 | 2026-02-16 09:45:13 | 1 | ||||||||
|
NeuroSynth Resource Report Resource Website 1000+ mentions |
NeuroSynth (RRID:SCR_006798) | Neurosynth | data or information resource, database, source code, software resource | Platform for large-scale, automated synthesis of functional magnetic resonance imaging (fMRI) data extracted from published articles. It''s a website wrapped around a set of open-source Python and JavaScript packages. Neurosynth lets you run crude but useful analyses of fMRI data on a very large scale. You can: * Interactively visualize the results of over 3,000 term-based meta-analyses * Select specific locations in the human brain and view associated terms * Browse through the nearly 10,000 studies in the database Their ultimate goal is to enable dynamic real-time analysis, so that you''ll be able to select foci, tables, or entire studies for analysis and run a full-blown meta-analysis without leaving your browser. You''ll also be able to do things like upload entirely new images and obtain probabilistic estimates of the cognitive states most likely to be associated with the image. | activation foci, magnetic resonance imaging assay, brain, human, fmri, neuroimaging, python, image, functional neuroimaging, FASEB list |
is used by: NeuroVault is used by: NIF Data Federation is listed by: GitHub is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Brainspell has parent organization: University of Texas at Austin; Texas; USA |
NIMH R01MH096906 | PMID:21706013 | Neurosynth Automated Coordinate Extraction (ACE) tools under, Open unspecified license, Open Software License, v3, Http://www.nitrc.org/include/glossary.php#552, Software is, Free, Copyright and permission notice required | nlx_55906 | http://www.nitrc.org/projects/neurosynth https://github.com/tyarkoni/neurosynth |
SCR_006798 | Neurosynth.org | 2026-02-16 09:46:48 | 1174 | ||||
|
HBM Hackathon Resource Report Resource Website 1+ mentions |
HBM Hackathon (RRID:SCR_014119) | meeting resource, training resource | A multi-day event hosted by the Organization for Human Brain Mapping which features collaborative and open neuroscience projects in data analysis and methods development. Locations change annually. | conference, human brain, meeting resource |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is affiliated with: brainhack.org |
Open to the neuroscience community (though a fee is required to attend) | http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3281 http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=1 |
SCR_014119 | OHBM Annual Meeting | 2026-02-16 09:48:30 | 6 | ||||||||
|
International Imaging Genetics Conference Resource Report Resource Website |
International Imaging Genetics Conference (RRID:SCR_014125) | meeting resource, training resource | An international symposium held initially to assess the new technology and innovation in the various established fields of genetics and imaging, and to facilitate the transdisciplinary fusion needed to optimize the development of the emerging field of Imaging Genetics. This annual conference features presentations from investigators world-wide and places emphasis on facilitating in-depth discussions among the participants and presenters. | meeting resource, symposium, international, imaging genetics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Irvine; California; USA |
http://www.imaginggenetics.uci.edu | SCR_014125 | 2026-02-16 09:48:36 | 0 | ||||||||||
|
CARLsim: a GPU-accelerated SNN Simulator Resource Report Resource Website 1+ mentions |
CARLsim: a GPU-accelerated SNN Simulator (RRID:SCR_014095) | software application, software resource, simulation software | A GPU-accelerated library for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail. CARLsim allows execution of networks of Izhikevich spiking neurons with realistic synaptic dynamics on both generic x86 CPUs and standard off-the-shelf GPUs. The simulator provides a PyNN-like programming interface in C/C++, which allows for details and parameters to be specified at the synapse, neuron, and network level. | simulation software, snn model, gpu accelerated, library, izhikevich spiking neuron, graphics processor, stdp, data parallelism |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Irvine; California; USA |
Available for download | http://www.socsci.uci.edu/~jkrichma/CARLsim/ | SCR_014095 | CARLsim | 2026-02-16 09:48:29 | 4 | ||||||||
|
Parallel Stochastic Ion Channel Simulator Resource Report Resource Website 1+ mentions |
Parallel Stochastic Ion Channel Simulator (RRID:SCR_014159) | PSICS | software application, software resource, simulation software | Software for efficient generation and simulation of models containing stochastic ion channels distributed across dendritic and axonal membranes. It computes the behavior of neurons taking account of the stochastic nature of ion channel gating and the detailed positions of the channels themselves. It is designed as a complement for existing tools. | simulation software, ion channel, dendritic membrane, axonal membrane, neuronal behavior, stochastic simulation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Edinburgh; Scotland; United Kingdom |
BBSRC | Public, Free | http://www.psics.org | SCR_014159 | 2026-02-16 09:48:31 | 1 |
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 2U24DK097771-09.
Email: info_at_ dknet.org
