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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Open Science Framework Resource Report Resource Website 500+ mentions |
Open Science Framework (RRID:SCR_003238) | OSF | service resource, data repository, storage service resource | Platform to support research and enable collaboration. Used to discover projects, data, materials, and collaborators helpful to your own research. | workflow, cloud, data management, provenance, network, collaboration, data sharing, interdisciplinary research, FASEB list |
is used by: NIH Heal Project is listed by: re3data.org is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: DataCite is listed by: FAIRsharing has parent organization: Center for Open Science |
Free, Freely available | DOI:10.25504/FAIRsharing.g4z879, DOI:10.17605, nlx_157292, DOI:10.17616/R3N03T, r3d100011268, SCR_017419 | http://openscienceframework.org https://doi.org/10.17616/R3N03T https://doi.org/10.17616/r3n03t https://doi.org/10.17605/ https://dx.doi.org/10.17605/ https://fairsharing.org/10.25504/FAIRsharing.g4z879 https://doi.org/10.17616/R35G9K |
SCR_003238 | 2026-02-16 09:46:01 | 741 | |||||||
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Statistics Online Computational Resource Resource Report Resource Website 10+ mentions |
Statistics Online Computational Resource (RRID:SCR_003378) | SOCR | software application, software toolkit, narrative resource, training material, software resource, data or information resource | A hierarchy of portable online interactive aids for motivating, modernizing probability and statistics applications. The tools and resources include a repository of interactive applets, computational and graphing tools, instructional and course materials. The core SOCR educational and computational components include the following suite of web-based Java applets: * Distributions (interactive graphs and calculators) * Experiments (virtual computer-generated games and processes) * Analyses (collection of common web-accessible tools for statistical data analysis) * Games (interfaces and simulations to real-life processes) * Modeler (tools for distribution, polynomial and spectral model-fitting and simulation) * Graphs, Plots and Charts (comprehensive web-based tools for exploratory data analysis), * Additional Tools (other statistical tools and resources) * SOCR Java-based Statistical Computing Libraries * SOCR Wiki (collaborative Wiki resource) * Educational Materials and Hands-on Activities (varieties of SOCR educational materials), * SOCR Statistical Consulting In addition, SOCR provides a suite of tools for volume-based statistical mapping (http://wiki.stat.ucla.edu/socr/index.php/SOCR_EduMaterials_AnalysesCommandLine) via command-line execution and via the LONI Pipeline workflows (http://www.nitrc.org/projects/pipeline). Course instructors and teachers will find the SOCR class notes and interactive tools useful for student motivation, concept demonstrations and for enhancing their technology based pedagogical approaches to any study of variation and uncertainty. Students and trainees may find the SOCR class notes, analyses, computational and graphing tools extremely useful in their learning/practicing pursuits. Model developers, software programmers and other engineering, biomedical and applied researchers may find the light-weight plug-in oriented SOCR computational libraries and infrastructure useful in their algorithm designs and research efforts. The three types of SOCR resources are: * Interactive Java applets: these include a number of different applets, simulations, demonstrations, virtual experiments, tools for data visualization and analysis, etc. All applets require a Java-enabled browser (if you see a blank screen, see the SOCR Feedback to find out how to configure your browser). * Instructional Resources: these include data, electronic textbooks, tutorials, etc. * Learning Activities: these include various interactive hands-on activities. * SOCR Video Tutorials (including general and tool-specific screencasts). | probability, statistics, instruction, statistical computing, applet, computational tool, graphing tool, course material, computation, java, statistical mapping, graphing, computational neuroscience, java, loni pipeline, educator, student, tool developer |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at Los Angeles; California; USA |
NIH Roadmap for Medical Research ; NSF 0442992; NSF DUE 0716055; NSF 1023115; NCRR U54 RR021813 |
PMID:21451741 PMID:21297884 |
Free, Freely available | nif-0000-32655 | http://www.nitrc.org/projects/socr | SCR_003378 | 2026-02-16 09:46:00 | 13 | |||||
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L-Measure Resource Report Resource Website 10+ mentions |
L-Measure (RRID:SCR_003487) | LM | software application, data processing software, image processing software, image analysis software, software resource, service resource | A freely available software tool available for the Windows and Linux platform, as well as the Online version Applet, for the analysis, comparison and search of digital reconstructions of neuronal morphologies. For the quantitative characterization of neuronal morphology, LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions, including: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available for either online use on any Java-enabled browser and platform or may be downloaded for local execution under Windows and Linux. | neuronal morphology, neuroinformatics, branching analysis, digital reconstruction, analysis, comparison, bio.tools |
is listed by: 3DVC is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: Computational Neuroanatomy Group |
Human Brain Project ; NINDS R01 NS39600 |
PMID:18451794 | Public | nif-0000-00003, biotools:l-measure | http://www.nitrc.org/projects/lmeasure https://bio.tools/l-measure |
SCR_003487 | 2026-02-16 09:46:09 | 30 | |||||
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Mouse Biomedical Informatics Research Network Resource Report Resource Website |
Mouse Biomedical Informatics Research Network (RRID:SCR_003392) | MouseBIRN, mBIRN | data set, reference atlas, data or information resource, atlas | Animal model data primarily focused on mice including high resolution MRI, light and electron microscopic data from normal and genetically modified mice. It also has atlases, and the Mouse BIRN Atlasing Toolkit (MBAT) which provides a 3D visual interface to spatially registered distributed brain data acquired across scales. The goal of the Mouse BIRN is to help scientists utilize model organism databases for analyzing experimental data. Mouse BIRN has ended. The next phase of this project is the Mouse Connectome Project (https://www.nitrc.org/projects/mcp/). The Mouse BIRN testbeds initially focused on mouse models of neurodegenerative diseases. Mouse BIRN testbed partners provide multi-modal, multi-scale reference image data of the mouse brain as well as genetic and genomic information linking genotype and brain phenotype. Researchers across six groups are pooling and analyzing multi-scale structural and functional data and integrating it with genomic and gene expression data acquired from the mouse brain. These correlated multi-scale analyses of data are providing a comprehensive basis upon which to interpret signals from the whole brain relative to the tissue and cellular alterations characteristic of the modeled disorder. BIRN's infrastructure is providing the collaborative tools to enable researchers with unique expertise and knowledge of the mouse an opportunity to work together on research relevant to pre-clinical mouse models of neurological disease. The Mouse BIRN also maintains a collaborative Web Wiki, which contains announcements, an FAQ, and much more. | electron microscopy, expression, functional, gene, 3-dimentional, brain, cellular, disorder, genomic, genotype, mouse, neurodegenerative disease, phenotype, molecular neuroanatomy resource, mri, light microscopy, model organism, gene expression, atlas data, imaging genomics, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Mouse BIRN Atlasing Toolkit is related to: Mouse Connectome Project has parent organization: Biomedical Informatics Research Network |
Normal, Neurodegenerative disease, Multiple Sclerosis, Alzheimer's disease, Parkinson's disease | NIH ; Collaborative Tools Support Network Award ; NCRR 1U24-RR025736; NCRR U24-RR021992; NCRR U24-RR021760; NCRR 1U24-RR026057-01 |
Free, Available for download, Freely available | nif-0000-00200 | https://loni.usc.edu/research/software?name=MBATWA | http://www.loni.ucla.edu/BIRN/Projects/Mouse/index.shtml | SCR_003392 | Mouse BIRN | 2026-02-16 09:46:07 | 0 | |||
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NIH Blueprint for Neuroscience Research Resource Report Resource Website 1+ mentions |
NIH Blueprint for Neuroscience Research (RRID:SCR_003670) | NIH Blueprint, Blueprint, | funding resource, training resource, topical portal, portal, data or information resource | Collaborative framework that includes the NIH Office of the Director and the 14 NIH Institutes and Centers that support research on the nervous system. By pooling resources and expertise, the Blueprint identifies cross-cutting areas of research, and confronts challenges too large for any single Institute or Center. The Blueprint makes collaboration a day-to-day part of how the NIH does business in neuroscience, complementing the basic missions of Blueprint partners. During each fiscal year, the partners contribute a small percentage of their funds to a common pool. Since the Blueprint's inception in 2004, this pool has comprised less than 1 percent of the total neuroscience research budget of the partners. In 2009, the Blueprint Grand Challenges were launched to catalyze research with the potential to transform our basic understanding of the brain and our approaches to treating brain disorders. * The Human Connectome Project is an effort to map the connections within the healthy brain. It is expected to help answer questions about how genes influence brain connectivity, and how this in turn relates to mood, personality and behavior. The investigators will collect brain imaging data, plus genetic and behavioral data from 1,200 adults. They are working to optimize brain imaging techniques to see the brain's wiring in unprecedented detail. * The Grand Challenge on Pain supports research to understand the changes in the nervous system that cause acute, temporary pain to become chronic. The initiative is supporting multi-investigator projects to partner researchers in the pain field with researchers in the neuroplasticity field. * The Blueprint Neurotherapeutics Network is helping small labs develop new drugs for nervous system disorders. The Network provides research funding, plus access to millions of dollars worth of services and expertise to assist in every step of the drug development process, from laboratory studies to preparation for clinical trials. Project teams across the U.S. have received funding to pursue drugs for conditions from vision loss to neurodegenerative disease to depression. Since its inception in 2004, the Blueprint has supported the development of new resources, tools and opportunities for neuroscientists. For example, the Blueprint supports several training programs to help students pursue interdisciplinary areas of neuroscience, and to bring students from underrepresented groups into the neurosciences. The Blueprint also funds efforts to develop new approaches to teaching neuroscience through K-12 instruction, museum exhibits and web-based platforms. From fiscal years 2007 to 2009, the Blueprint focused on three major themes of neuroscience - neurodegeneration, neurodevelopment, and neuroplasticity. These efforts enabled unique funding opportunities and training programs, and helped establish new resources including the Blueprint Non-Human Primate Brain Atlas. | animal model, collaboration, computational biology, imaging tool, initiative, neurodegeneration, neurodevelopment, neuroinformatics, brain, brain disorder, pain, drug, nervous system disorder, neurotherapeutics, neuroplasticity, neuroscience |
has parent organization: National Institutes of Health is parent organization of: CRE Driver Network is parent organization of: Blueprint Neurotherapeutics Network is parent organization of: National Center for Complementary and Alternative Medicine is parent organization of: National Eye Institute (NEI) Commons is parent organization of: National Institute of Biomedical Imaging and Bioengineering is parent organization of: National Institute of Nursing Research is parent organization of: National Institute on Alcohol Abuse and Alcoholism is parent organization of: National Institute on Drug Abuse is parent organization of: National Institute on Deafness and Other Communication Disorders is parent organization of: National Institute of General Medical Sciences is parent organization of: National Institute of Dental and Craniofacial Research is parent organization of: Office of Behavioral and Social Sciences Research is parent organization of: National Institute of Child Health and Human Development is parent organization of: National Institute of Environmental Health Sciences is parent organization of: National Institute of Mental Health is parent organization of: National Institute on Aging is parent organization of: National Institute of Neurological Disorders and Stroke is parent organization of: NeuroImaging Tools and Resources Collaboratory (NITRC) |
nif-0000-00219 | SCR_003670 | Neuroscience Blueprint | 2026-02-16 09:46:10 | 9 | ||||||||
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Open Connectome Project Resource Report Resource Website 1+ mentions |
Open Connectome Project (RRID:SCR_004232) | Open Connectome Project | web service, image repository, data set, data analysis service, analysis service resource, data access protocol, data repository, software resource, storage service resource, source code, production service resource, service resource, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Connectomes repository to facilitate the analysis of connectome data by providing a unified front for connectomics research. With a focus on Electron Microscopy (EM) data and various forms of Magnetic Resonance (MR) data, the project aims to make state-of-the-art neuroscience open to anybody with computer access, regardless of knowledge, training, background, etc. Open science means open to view, play, analyze, contribute, anything. Access to high resolution neuroanatomical images that can be used to explore connectomes and programmatic access to this data for human and machine annotation are provided, with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access, so collectively, we can begin to unravel connectomes. Services: * Data Hosting - Their Bruster (brain-cluster) is large enough to store nearly any modern connectome data set. Contact them to make your data available to others for any purpose, including gaining access to state-of-the-art analysis and machine vision pipelines. * Web Viewing - Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by Google Maps, enhanced to allow the exploration of 3D image data. View the fork of the code or go directly to view the data. * Volume Cutout Service - RESTful API that enables you to select any arbitrary volume of the 3d database (3ddb), and receive a link to download an HDF5 file (for matlab, C, C++, or C#) or a NumPy pickle (for python). Use some other programming language? Just let them know. * Annotation Database - Spatially co-registered volumetric annotations are compactly stored for efficient queries such as: find all synapses, or which neurons synapse onto this one. Create your own annotations or browse others. *Sample Downloads - In addition to being able to select arbitrary downloads from the datasets, they have also collected a few choice volumes of interest. * Volume Viewer - A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels. The code and program can be downloaded. * Machine Vision Pipeline - They are building a machine vision pipeline that pulls volumes from the 3ddb and outputs neural circuits. - a work in progress. As soon as we have a stable version, it will be released. * Mr. Cap - The Magnetic Resonance Connectome Automated Pipeline (Mr. Cap) is built on JIST/MIPAV for high-throughput estimation of connectomes from diffusion and structural imaging data. * Graph Invariant Computation - Upload your graphs or streamlines, and download some invariants. * iPad App - WholeSlide is an iPad app that accesses utilizes our open data and API to serve images on the go. | human, primary visual cortex, data sharing, male, electron microscopy, mri, connectome, annotation, image collection, array tomography |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CATMAID is related to: neurodata is parent organization of: Rambo3D |
Johns Hopkins University; Maryland; USA ; JHU Applied Research Laboratory IRAD ; JHU Whiting School of Engineering ; Dean's Award ; NIBIB 1RO1EB016411-01 (CRCNS); DARPA N66001-14-1-4028 (GRAPHS); NSF ACI-1261715; NSF OCI-1040114; NIDA 1R01DA036400-01; |
PMID:23707591 | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000189, nlx_143645 | http://openconnecto.me http://www.nitrc.org/projects/ocp/ |
SCR_004232 | openconnectomeproject, Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time., Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time | 2026-02-16 09:46:17 | 7 | ||||
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Federal Interagency Traumatic Brain Injury Research Informatics System Resource Report Resource Website 50+ mentions |
Federal Interagency Traumatic Brain Injury Research Informatics System (RRID:SCR_006856) | FITBIR | narrative resource, data repository, database, storage service resource, topical portal, portal, service resource, data or information resource, standard specification | Platform for Traumatic Brain Injury relevant data. System was developed to share data across entire TBI research field and to facilitate collaboration between laboratories and interconnectivity between informatics platforms. FITBIR implements interagency Common Data Elements for TBI research and provides tools and resources to extend data dictionary. Established submission strategy to ensure high quality and to provide maximum benefit to investigators. Qualified researchers can request access to data stored in FITBIR and/or data stored at federated repositories. | Traumatic, brain, injury, platform, common, data, element, medical, imaging, clinical, assessment, environment, behavior, brain, magnetic, resonance |
is recommended by: National Library of Medicine is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: NIH Data Sharing Repositories is related to: NIH Data Sharing Repositories has parent organization: Center for Information Technology |
Traumatic Brain Injury | NINDS ; U.S. Army Medical Research and Material Command ; Center for Information Technology |
Restricted | nlx_151755, r3d100012837 | https://doi.org/10.17616/R31NJMED | SCR_006856 | Federal Interagency Traumatic Brain Injury Research (FITBIR) Informatics System, FITBIR Informatics System | 2026-02-16 09:46:49 | 57 | ||||
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Scalable Brain Atlas Resource Report Resource Website 10+ mentions |
Scalable Brain Atlas (RRID:SCR_006934) | SBA | software application, reference atlas, atlas, software resource, service resource, data or information resource | A web-based, interactive brain atlas viewer, containing a growing number of atlas templates for various species, including mouse, macaque and human. Standard features include fast brain region lookup, point and click to select a region and view its full 3D extent, mark a stereotaxic coordinate and view all regions in a hierarchy. Built-in extensions are the CoCoMac plugin, which provides a spatial display of Macaque connectivity, and a service to transform stereotaxic coordinates to and from the INCF Waxholm space for the mouse. Three dimensional renderings of brain regions are available through a Matlab interface (local installation of Matlab required). The SBA is designed to be customizable. External users can create plugins, hosted on their own servers, to interactively attach images or data to spatial atlas locations. This fully web-based display engine for brain atlases and topologies allows client websites to show brain region related data in a 3D interactive context. Currently available atlases are: * Macaque: The Paxinos Rhesus Monkey atlas (2000) * Macaque: Various templates available through Caret, registered to F99 space: Felleman and Van Essen (1991), Lewis and Van Essen (2000), Regional Map from K��tter and Wanke (2005), Paxinos Rhesus Monkey (2000) * Macaque: The NeuroMaps Macaque atlas (2008) * Mouse: The INCF Waxholm Space for the mouse (2011). Previous versions available. * Mouse: The Allen Mouse Brain volumetric atlas (ABA07) * Human: The LPBA40 parcellation, registered to SRI24 space A variety of services are being developed around the templates contained in the Scalable Brain Atlas. For example, you can include thumbnails of brain regions in your own webpage. Other applications include: * Analyze atlas templates in Matlab * List all regions belonging to the given template * List of supported atlas templates * Find region by coordinate * Color-coded PNG (bitmap) or SVG (vector) image of a brain atlas slice * Region thumbnail in 2D (slice) or 3D (stack of slices) The Scalable Brain Atlas is created by Rembrandt Bakker and Gleb Bezgin, under supervision of Rolf K��tter in the NeuroPhysiology and -Informatics group of the Donders Institute, Radboud UMC Nijmegen. | atlas application, atlas data, image display, javascript, magnetic resonance, os independent, php, three dimensional display, tractography, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: CoCoMac is related to: 3DBar has parent organization: International Neuroinformatics Coordinating Facility |
International Neuroinformatics Coordinating Facility | GNU General Public License | nlx_98156 | http://www.nitrc.org/projects/sba | SCR_006934 | INCF Scalable Brain Atlas | 2026-02-16 09:46:50 | 21 | |||||
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NeuroPub Visualizer Resource Report Resource Website |
NeuroPub Visualizer (RRID:SCR_006797) | NeuroPub | software application, data processing software, data visualization software, software resource, mobile app | A NIfTI visualizer for statistical brain images (fMRI, VBM, etc) the iPad. The visualizer displays these images as overlay on the MNI standard brain. You can use it to store all your statistical images from your fMRI / VBM / TBSS studies and visualise them in 2D and 3D. Use NeuroPub as a library for your statistical images. It's the perfect app to bring to meetings, conferences, etc, and show your latest results. | magnetic resonance, fmri, vbm, tbss | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | nlx_155827 | http://www.nitrc.org/projects/neuropub | SCR_006797 | 2026-02-16 09:46:48 | 0 | |||||||
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Cambridge Brain Activation Resource Report Resource Website 10+ mentions |
Cambridge Brain Activation (RRID:SCR_007109) | CamBA | software application, data processing software, software toolkit, image analysis software, software resource, workflow software | Suite of programs developed for fMRI analysis in a Virtual Pipeline Laboratory facilitates combining program modules from different software packages into processing pipelines to create analysis solutions which are not possible with a single software package alone. Current pipelines include fMRI analysis, statistical testing based on randomization methods and fractal spectral analysis. Pipelines are continually being added. The software is mostly written in C. This fMRI analysis package supports batch processing and comprises the following general functions at the first level of individual image analysis: movement correction (interpolation and regression), time series modeling, data resampling in the wavelet domain, hypothesis testing at voxel and cluster levels. Additionally, there is code for second level analysis - group and factorial or ANOVA mapping - after co-registration of voxel statistic maps from individual images in a standard space. The main point of difference from other fMRI analysis packages is the emphasis throughout on the use of data resampling (permutation or randomization) as a basis for inference on individual, group and factorial test statistics at voxel and cluster levels of resolution. | analysis, brain, anova, resampling, statistical, wavelet, fmri, pipeline, affine warp, algorithm or reusable library, application, c, image-to-template, java, linux, macos, magnetic resonance, nifti-1, posix/unix-like, registration, regression, spatial transformation, spectral analysis, statistical operation, temporal transformation, time domain analysis, unix shell, warping, wavelet transformation, web environment |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of Cambridge; Cambridge; United Kingdom |
GlaxoSmithKline ; Human Brain Project ; NIMH ; NIBIB |
GNU General Public License | nif-0000-00267 | http://www-bmu.psychiatry.cam.ac.uk/software/ | SCR_007109 | 2026-02-16 09:46:53 | 11 | ||||||
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ABSORB: Atlas Building by Self-Organized Registration and Bundling Resource Report Resource Website 1+ mentions |
ABSORB: Atlas Building by Self-Organized Registration and Bundling (RRID:SCR_007018) | ABSORB | software application, data processing software, registration software, image analysis software, software resource, source code | This software package implements an algorithm for effective groupwise registration. The required input is a set of 3D MR intensity images (in Analyze format with paired .hdr and .img files) with a text file (.txt) listing all header file (.hdr) names. The output is the set of registered images together with the corresponding dense deformation fields. This software has been tested on Windows XP (32-bit) and Linux (64-bit, kernel version 2.6.18-194.el5). The images should be pre-processed before applying ABSORB: * All brain MR images used as inputs to ABSORB should be in the same situation (e.g., skull-stripped or not, cerebellum removed or not, etc.). * The input images should be in Analyze format with paired header and image files. This software was developed in IDEA group in UNC-Chapel Hill. | image, registration, bundling, atlas, magnetic resonance, algorithm or reusable library, intermodal, intersubject, intrasubject, image-to-template, affine warp, nonlinear warp |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA |
PMID:20226255 | Free, Public | nlx_144409 | http://www.nitrc.org/projects/absorb | SCR_007018 | ABSORB: Atlas Building by Self-Organized Registration Bundling, Atlas Building by Self-Organized Registration Bundling, Atlas Building by Self-Organized Registration and Bundling | 2026-02-16 09:46:51 | 1 | |||||
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Matlab Neuroshare Library Resource Report Resource Website |
Matlab Neuroshare Library (RRID:SCR_006957) | NeuroshareLibrary | software resource, software toolkit, software library | This is MATLAB library to create Neuroshare data format. You can convert your own data into Neuroshare format file. | console (text based), eeg, meg, electrocorticography, format conversion, japanese, linux, macos, matlab, microsoft, posix/unix-like, windows, neuroshare, data format, data sharing |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: ATR; Kyoto; Japan |
Japanese Ministry of Education Culture Sports Science and Technology MEXT | GNU General Public License | nlx_155880 | http://www.nitrc.org/projects/nslib_v1_3_1 | SCR_006957 | Neuroshare Library | 2026-02-16 09:46:50 | 0 | |||||
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fMRI Data Center Resource Report Resource Website 10+ mentions |
fMRI Data Center (RRID:SCR_007278) | fMRIDC | data repository, database, storage service resource, service resource, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2013 Public curated repository of peer reviewed fMRI studies and their underlying data. This Web-accessible database has data mining capabilities and the means to deliver requested data to the user (via Web, CD, or digital tape). Datasets available: 107 NOTE: The fMRIDC is down temporarily while it moves to a new home at UCLA. Check back again in late Jan 2013! The goal of the Center is to help speed the progress and the understanding of cognitive processes and the neural substrates that underlie them by: * Providing a publicly accessible repository of peer-reviewed fMRI studies. * Providing all data necessary to interpret, analyze, and replicate these fMRI studies. * Provide training for both the academic and professional communities. The Center will accept data from those researchers who are publishing fMRI imaging articles in peer-reviewed journals. The goal is to serve the entire fMRI community. | fmri, cognitive, cortex, mri, talairach, neuroimaging, cognitive neuroscience, brain, structure, function, magnetic resonance, intellect, image collection, data set |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: re3data.org has parent organization: University of California at Santa Barbara; California; USA |
NSF ; W. M. Keck Foundation ; NIMH ; Sun Microsystems Center of Excellence |
PMID:11545705 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00025 | http://www.fmridc.org/ | SCR_007278 | The fMRI Data Center | 2026-02-16 09:46:56 | 16 | ||||
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National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) Resource Report Resource Website 50+ mentions |
National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS) (RRID:SCR_007314) | NIAGADS | data set, data repository, database, storage service resource, service resource, data or information resource | National genetics data repository facilitating access to genotypic and phenotypic data for Alzheimer's disease (AD). Data include GWAS, whole genome (WGS) and whole exome (WES), expression, RNA Seq, and CHIP Seq analyses. Data for the Alzheimer’s Disease Sequencing Project (ADSP) are available through a partnership with dbGaP (ADSP at dbGaP). Repository for many types of data generated from NIA supported grants and/or NIA funded biological samples. Data are deposited at NIAGADS or NIA-approved sites. Genetic Data and associated Phenotypic Data are available to qualified investigators in scientific community for secondary analysis. | genetics, alzheimer's disease, genome-wide association study, neurodegenerative disease, genotype, phenotype, late adult human, dna marker, dna sequencing, rna expression, rna, dna, gene |
is recommended by: National Library of Medicine is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NIH Data Sharing Repositories is related to: Allen Institute for Brain Science has parent organization: University of Pennsylvania Perelman School of Medicine; Pennsylvania; USA |
Alzheimer's disease, Late-onset Alzheimer's disease, Aging | NIH Blueprint for Neuroscience Research ; NIA U24 AG041689; NIA 3U24AG041689 |
nif-0000-00179 | http://www.nitrc.org/projects/niagads http://alois.med.upenn.edu/niagads/ | SCR_007314 | National Institute on Aging, NIA Genetics of Alzheimer's Disease Data Storage Site, Genetics of Alzheimer’s Disease Data Storage Site | 2026-02-16 09:46:56 | 60 | |||||
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neuroConstruct Resource Report Resource Website 10+ mentions |
neuroConstruct (RRID:SCR_007197) | neuroConstruct | software application, software resource, simulation software | Software for simulating complex networks of biologically realistic neurons, i.e. models incorporating dendritic morphologies and realistic cell membrane conductance, implemented in Java and generates script files for the NEURON and GENESIS simulators, with support for other simulation platforms (including PSICS and PyNN) in development. neuroConstruct is being developed in the Silver Lab in the Department of Neuroscience, Physiology and Pharmacology at UCL and uses the latest NeuroML specifications, including MorphML, ChannelML and NetworkML. Some of the key features of neuroConstruct are: Creation of networks of biologically realistic neurons, positioned in 3D space. Complex connectivity patterns between cell groups can be specified for the networks. Can import morphology files in GENESIS, NEURON, Neurolucida, SWC and MorphML format for inclusion in network models. Simulations can be run on the NEURON or GENESIS platforms. Cellular processes (synapses/channel mechanisms) can be imported from native script files or created in ChannelML. Recording of simulation data generated by the simulation and visualization/analysis of data. Stored simulation runs can be viewed and managed through the Simulation Browser interface. | cell, cellular, channel, conductance, data, dendrite, java, mechanism, membrane, model, morphology, network, neuron, neuronal network, pharmacology, physiology, simulation, software, synapse, visualization |
is listed by: 3DVC is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NEURON is related to: Open Source Brain is related to: NeuroML has parent organization: University College London; London; United Kingdom |
Wellcome Trust ; MRC |
nif-0000-00105 | http://www.nitrc.org/projects/neuroconstruct | SCR_007197 | neuroConstruct: Biophysical Neural Network Modeling Software | 2026-02-16 09:46:54 | 10 | ||||||
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NeuroLens Resource Report Resource Website 1+ mentions |
NeuroLens (RRID:SCR_007372) | NeuroLens | software application, data processing software, data visualization software, image processing software, image analysis software, software resource | An integrated environment for the analysis and visualization of functional neuroimages. It is intended to provide extremely fast and flexible image processing, via an intuitive user interface that encourages experimentation with analysis parameters and detailed inspection of both raw image data and processing results. All processing operations in NeuroLens are built around a Plugin architecture, making it easy to extend its functionality. NeuroLens runs on Apple computers based on the G4, G5, or Intel chipsets and running MacOSX 10.4 (Tiger) or later. It is available free for academic and non-profit research use. * Operating System: MacOS * Programming Language: Objective C * Supported Data Format: AFNI BRIK, ANALYZE, COR, DICOM, MGH/MGZ, MINC, Other Format | image-to-image, linear, temporal convolution - deconvolution, multivariate analysis, neuroimaging, fmri, brain structure, neural structure, brain, temporal convolution, temporal deconvolution, afni brik, analyze, cor, dicom, image display, macos, mgh/mgz, minc, magnetic resonance, objective c, registration, regression, rendering, software, spatial transformation, statistical operation, surface rendering, temporal transformation, three dimensional display, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of Montreal; Quebec; Canada |
MGH CSRL License, - free for academic and non-profit research use. | nif-0000-00333 | http://www.nitrc.org/projects/nldo | SCR_007372 | 2026-02-16 09:46:57 | 9 | |||||||
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Neuroimaging in Python Resource Report Resource Website 10+ mentions |
Neuroimaging in Python (RRID:SCR_013141) | NIPY, | software development tool, software application, software development environment, community building portal, software resource, portal, data or information resource | Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration. | brain, imaging, neuroimaging, analysis, python, fmri, fmri analysis, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Python Programming Language has parent organization: SourceForge has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; is parent organization of: Dipy is parent organization of: NiLearn is parent organization of: NIPY is parent organization of: NiBabel is parent organization of: Nipype is parent organization of: Nitime |
NIMH 5R01MH081909-02; NIBIB 1R03EB008673-01 |
PMID:21897815 | Revised BSD license | nlx_149365 | http://www.nitrc.org/projects/nipy-community http://www.nitrc.org/projects/nipype | SCR_013141 | NIPY Community | 2026-02-16 09:48:33 | 24 | ||||
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AngioCalc Cerebral Aneurysm Calculator Resource Report Resource Website 1+ mentions |
AngioCalc Cerebral Aneurysm Calculator (RRID:SCR_012805) | AngioCalc | software application, software resource, data management software | Providing quality resources for the management of cerebral aneurysms and features an online calculator that calculates cerebral aneurysm volume and percent packing volume after coil embolization. The site also host an imaging Library with neuroanatomy and neurovascular images. | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | nlx_155693 | SCR_012805 | AngioCalc Cerebral and Peripheral Aneurysm Calculator, AngioCalc Cerebral Aneurysm Calculator | 2026-02-16 09:48:30 | 9 | |||||||||
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USC Multimodal Connectivity Database Resource Report Resource Website 10+ mentions |
USC Multimodal Connectivity Database (RRID:SCR_012809) | UMCD | data repository, database, storage service resource, service resource, data or information resource | Web-based repository and analysis site for connectivity matrices that have been derived from neuroimaging data including different imaging modalities, subject groups, and studies. Users can analyze connectivity matrices that have been shared publicly and upload their own matrices to share or analyze privately. | fmri, dti, dsi, mri, eeg, meg, data set, image, computational hosting, connectivity, neuroimaging, data sharing, brain, rendering, diffusion-weighted mri, functional connectivity, graph theory, resting-state fmri, structural connectivity, image display, magnetic resonance, python, rendering, visualization, connectivity matrix, network, brain network, matrix, de-identified, male, female, apoe, child, adult |
is used by: NIF Data Federation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: MGH-USC Human Connectome Project |
Normal, Lesioned, Attention deficit-hyperactivity disorder, Autism Spectrum Disorder, Obsessive-Compulsive Disorder, BDD, APOE 4/4, APOE 3/4, APOE 3/3, Alzheimer's disease | NRSA ; NIH Blueprint for Neuroscience Research ; NIA F31AG035438-01; NIDA HHSN271200800035C |
PMID:23226127 PMID:20850551 |
The community can contribute to this resource, Some features require an account | nlx_83091 | http://www.nitrc.org/projects/umcd | http://jessebrown.webfactional.com/welcome/default/index | SCR_012809 | UCLA Connectivity Database, UCLA Multimodal Connectivity Database: Web-based brain network analysis and data sharing, UCLA Multimodal Connectivity Database | 2026-02-16 09:48:17 | 25 | ||
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LiverSegm Resource Report Resource Website |
LiverSegm (RRID:SCR_013108) | LiverSegm | software application, data processing software, image processing software, image analysis software, software resource, segmentation software | A set of tools for the processing of liver images. These tools consist of a level set based variational approach that incorporates shape priors and appearance models. It uses ITK-SNAP 1.4 as interface. The tools are capable of automatic liver segmentation and semi-automatic injury segmentation. | liver segmentation, image processing software, injury segmentation |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: ITK-SNAP |
Free | nlx_155788 | SCR_013108 | 2026-02-16 09:48:20 | 0 |
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