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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) Resource Report Resource Website 10+ mentions |
Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR) (RRID:SCR_002517) | PDBP | material storage repository, biospecimen repository, storage service resource, service resource | Common data management resource and web portal to promote discovery of Parkinson's Disease diagnostic and progression biomarker candidates for early detection and measurement of disease progression. PDBP will serve as multi-faceted platform for integrating existing biomarker efforts, standardizing data collection and management across these efforts, accelerating discovery of new biomarkers, and fostering and expanding collaborative opportunities for all stakeholders. | parkinson's, clinical neuroinformatics, magnetic resonance, diagnostic, progression, biomarker, clinical |
is recommended by: National Library of Medicine is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NINDS Repository is related to: MIPAV: Medical Image Processing and Visualization has parent organization: National Institute of Neurological Disorders and Stroke |
Parkinson's disease | nlm ; NINDS |
PMID:25976927 | Restricted | nlx_155919 | http://www.nitrc.org/projects/pdbp | http://pdbp.ninds.nih.gov/index.jsp | SCR_002517 | Parkinson's Disease Biomarkers Program, PDBP: Parkinsons Disease Biomarkers Program, Parkinson’s Disease Biomarkers Program Data Management Resource, PDBP DMR | 2026-02-14 02:00:17 | 24 | ||
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Subject Library Resource Report Resource Website |
Subject Library (RRID:SCR_002595) | Subject Library | data processing software, software library, data management software, software toolkit, software application, image processing software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A collection of software tools used for processing and organizing MRI data. The Dicom Importer allows you to to view, assemble, and organize dicom files. Subject Library is a filesystem-based search and reporting tool that can be configured to work with many different organization schemes. This package also contains a python library that can be used to write scripts for custom tasks. | reusable library, analyze, database application, magnetic resonance, os independent, python, workflow, mri, organize, process, neuroimaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Davis; California; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155999 | http://www.nitrc.org/projects/subjectlibrary | SCR_002595 | 2026-02-14 02:00:27 | 0 | |||||||
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PANDA Resource Report Resource Website 100+ mentions |
PANDA (RRID:SCR_002511) | PANDA | software resource, software toolkit | Software matlab toolbox for pipeline processing of diffusion MRI images. For each subject, PANDA can provide outputs in 2 types: i) diffusion parameter data that is ready for statistical analysis; ii) brain anatomical networks constructed by using diffusion tractography. Particularly, there are 3 types of resultant diffusion parameter data: WM atlas-level, voxel-level and TBSS-level. The brain network generated by PANDA has various edge definitions, e.g. fiber number, length, or FA-weighted. The key advantages of PANDA are as follows: # fully-automatic processing from raw DICOM/NIFTI to final outputs; # Supporting both sequential and parallel computation. The parallel environment can be a single desktop with multiple-cores or a computing cluster with a SGE system; # A very friendly GUI (graphical user interface). | analyze, computational neuroscience, connectivity analysis, dicom, format conversion, gnome, linux, macos, matlab, modeling, magnetic resonance, nifti, posix/unix-like, tensor metric, tractography, workflow, xnat pipeline, diffusion mri, chinese, connectome, diffusion metrics, network, pipeline, structural connectivity |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Beijing Normal University; Beijing; China |
National Natural Science Foundation of China ; Beijing Nova Program ; 973 program ; State Key Laboratory of Cognitive Neuroscience and Learning |
PMID:23439846 | Free, Available for download, Freely available | nlx_155911 | http://www.nitrc.org/projects/panda | SCR_002511 | PANDA: a pipeline tool for diffusion MRI, PANDA (Pipeline for Analyzing braiN Diffusion imAges), Pipeline for Analyzing braiN Diffusion imAges, PANDA: Pipeline for Analyzing braiN Diffusion imAges, panda-tool | 2026-02-14 02:00:17 | 376 | ||||
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TAPIR Resource Report Resource Website 50+ mentions |
TAPIR (RRID:SCR_002596) | TAPIR | data processing software, software application, registration software, software resource, image analysis software | A set of command line tools allowing 2D and 3D image registration, mainly for medical imaging (although also relevant to other image registration problems). | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | nlx_156001 | SCR_002596 | Tools for Advanced Parameterized Image Registration | 2026-02-14 02:00:17 | 66 | |||||||
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Segmentation Validation Engine Resource Report Resource Website |
Segmentation Validation Engine (RRID:SCR_002591) | SVE | data analysis service, analysis service resource, production service resource, service resource, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An automated online framework for performing validation studies of skull-stripping methods. Registered users may download 40 T1 MRI volumes, skull-strip them with the algorithm of their choice, and upload their segmentation results to the SVE website. The server will then compare the 40 skull-stripped results against a set of manually generated brain masks. The server computes a series of measures for the uploaded data, including Jaccard and Dice measures. It also produces images for visualizing the spatial location of the segmentation errors relative to a common space. The results are archived on the server, and the measures are viewable by visitors to the site. | analyze, dice coefficient, information resource, loni/sve terms of use, magnetic resonance, nifti, os independent, other/proprietary license, overlap metrics, quality metrics, quantification, segmentation, tanomoto coefficient, web environment, web resource, web service, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of California at Los Angeles; California; USA |
PMID:19073267 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155995 | http://www.nitrc.org/projects/sve | SCR_002591 | 2026-02-14 02:00:17 | 0 | ||||||
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Nirfast Resource Report Resource Website 10+ mentions |
Nirfast (RRID:SCR_002503) | NIRFAST | software resource, software toolkit | Software package for modeling Near-Infrared light transport in tissue and image reconstruction. This includes: Standard single wavelength absorption and reduced scatter, Multi-wavelength spectrally constrained models and Fluorescence models. | optical imaging, tissue |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Dartmouth College; New Hampshire; USA |
PMID:20182646 PMID:23942632 |
Free, Available for download, Freely available | nlx_155902 | http://www.nitrc.org/projects/nirfast | SCR_002503 | 2026-02-14 02:00:24 | 35 | ||||||
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Web Interfaces for Multiscale Images Resource Report Resource Website |
Web Interfaces for Multiscale Images (RRID:SCR_002589) | Web Interfaces for Multiscale Images | knowledge environment | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Venue for discussing and defining standard web interfaces for sharing images, annotations, and analyses of multiscale biological images. The goal is to increase interoperability of code to share the burden of infrastructure, increase code reuse, and allow us to spend more time focused on scientific questions. Please visit our Wiki to start participating. Together we can develop a small group of interfaces which are easy to implement, extensible, and cover the major tasks of developing tools for multiscale data on the web. | magnetic resonance, interoperability, microscopy, standard specification, forum | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156020 | SCR_002589 | 2026-02-14 02:00:27 | 0 | ||||||||
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OEI fMRI compatible olfactometer Resource Report Resource Website 1+ mentions |
OEI fMRI compatible olfactometer (RRID:SCR_002507) | OEI fMRI compatible olfactometer | instrument resource | A computerized, odor delivery device that can be used for basic research applications including mapping olfactory centers, cognitive / learning research, neuro-marketing among other uses. Additional products including tests for odor threshold, odor identification, odor discrimination and odor memory. | experiment control, hardware, magnetic resonance, stimulus presentation, odor, olfactory, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial License | nlx_155907 | http://www.nitrc.org/projects/oei http://www.osmicenterprises.com/docs/OsmicFMRIOlfactomterManual%207-1-13.pdf |
SCR_002507 | 2026-02-14 02:00:26 | 4 | |||||||
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Non-Rigid Image Registration Evaluation Project Resource Report Resource Website 1+ mentions |
Non-Rigid Image Registration Evaluation Project (RRID:SCR_002505) | NIREP | data or information resource, software resource, narrative resource, database, standard specification | Project to develop software tools and provide shared image validation databases for rigorous testing of non-rigid image registration algorithms. NIREP will extend the scope of prior validation projects by developing evaluation criteria and metrics using large image populations, using richly annotated image databases, using computer simulated data, and increasing the number and types of evaluation criteria. The goal of this project is to establish, maintain, and endorse a standardized set of relevant benchmarks and metrics for performance evaluation of nonrigid image registration algorithms. Furthermore, these standards will be incorporated into an exportable computer program to automatically evaluate the registration accuracy of nonrigid image registration algorithms. | magnetic resonance, registration software |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Iowa; Iowa; USA |
NIBIB R33 EB004126 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155904 | http://www.nitrc.org/projects/nirep | SCR_002505 | Non-Rigid Image Registration Evaluation Project, Non-Rigid Image Registration Evaluation Project (NIREP) | 2026-02-14 02:00:25 | 7 | |||||
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Cognitive Atlas Resource Report Resource Website 10+ mentions |
Cognitive Atlas (RRID:SCR_002793) | Cognitive Atlas | data or information resource, ontology, controlled vocabulary | Knowledge base (or ontology) that characterizes the state of current thought in cognitive science that captures knowledge from users with expertise in psychology, cognitive science, and neuroscience. There are two basic kinds of knowledge in the knowledge base. Terms provide definitions and properties for individual concepts and tasks. Assertions describe relations between terms in the same way that a sentence describes relations between parts of speech. The goal is to develop a knowledge base that will support annotation of data in databases, as well as supporting improved discourse in the community. It is open to all interested researchers. A fundamental feature of the knowledge base is the desire and ability to capture not just agreement but also disagreement regarding definitions and assertions. Thus, if you see a definition or assertion that you disagree with, then you can assert and describe your disagreement. The project is led by Russell Poldrack, Professor of Psychology and Neurobiology at the University of Texas at Austin in collaboration with the UCLA Center for Computational Biology (A. Toga, PI) and UCLA Consortium for Neuropsychiatric Phenomics (R. Bilder, PI). Most tasks used in cognitive psychology research are not identical across different laboratories or even within the same laboratory over time. A major advantage of anchoring cognitive ontologies to the measurement level is that the strategy for determining changes in task properties is easier than tracking changes in concept definitions and usage. The process is easier because task parameters are usually (if not always) operationalized objectively, offering a clear basis to judge divergence in methods. The process is also easier because most tasks are based on prior tasks, and thus can more readily be considered descendants in a phylogenetic sense. | cognitive function, cognitive phenotype, cognitive process, cognitive science, cognitive state, human, cognitive ontology, cognitive task, experimental task, mental construct, concept, task, eeg, meg, electrocorticography, magnetic resonance, ontology, pet, spect, knowledge environment |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Speech Perception is related to: Brainspell has parent organization: University of Texas at Austin; Texas; USA is parent organization of: Cognitive Atlas Ontology |
NIMH RO1MH082795 | PMID:21922006 PMID:19634038 |
Free, Freely Available | nif-0000-24591 | http://www.nitrc.org/projects/cogatlas | SCR_002793 | cognitive atlas - a collaboratively developed cognitive science ontology | 2026-02-14 02:00:32 | 32 | ||||
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FFT Library Resource Report Resource Website |
FFT Library (RRID:SCR_002698) | FFT Library | data processing software, software library, software toolkit, software application, image processing software, software resource | Java library used for the execution of discrete Fourier transforms in 1-D, 2-D and 3-D through the implementation of Fast Fourier Transform (FFT) algorithms. * The FFT library has been written in Java for portability across different platforms, integrated into a single jar file for easy implementation. * The FFT library provides forward and backward fast Fourier transforms in 1-D, 2-D and 3-D with an easy-to-use manner. * The FFT requires the length equal to a number with an integer power of two. This library automatically examines the input data and detects the length to prevent improper execution. | fourier transform, fast fourier transform, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: Laboratory of Neuro Imaging |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15; NCRR U54 RR021813 |
PMID:24822428 | Free, Freely available | nif-0000-23324 | http://www.nitrc.org/projects/fft http://www.loni.ucla.edu/Software/FFT | SCR_002698 | Fast Fourier Transform JavaLibrary, FFT Java library, Fast Fourier Transform Library, Fast Fourier Transform (FFT) JavaLibrary | 2026-02-14 02:00:18 | 0 | ||||
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LONI ShapeViewer Resource Report Resource Website |
LONI ShapeViewer (RRID:SCR_002695) | data visualization software, software resource, data processing software, software application | Java-based geometry viewer that supports file formats used by Center for Computational Biology (CCB) researchers and provides necessary viewing functions. ShapeViewer uses ShapeTools library support to read and display LONI Ucf, VTX XML, FreeSurfer, Minc Obj (both binary and ascii), Open Dx, Gifti, and OFF format data files. | ccb license, manifold viewer, computed tomography, magnetic resonance, pet, java |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: LONI ShapeTools has parent organization: Laboratory of Neuro Imaging |
NCRR U54 RR021813 | Free, Available for download, Freely available | nif-0000-23321 | SCR_002695 | ShapeViewer, LONI Shape Viewer | 2026-02-14 02:00:30 | 0 | |||||||
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Synchronized Histological Image Viewing Architecture Resource Report Resource Website |
Synchronized Histological Image Viewing Architecture (RRID:SCR_002690) | SHIVA | data processing software, d visualization software, software application, image processing software, software resource, image analysis software | A Java-based visualization and analysis application that can process 2D and 3D image files and provides convenient methods for users to overlay multiple datasets. * Simultaneous visualization of multiple image volumes. * Tools for labeling and masking of structures. * Framework for the Mouse Atlas Project. | data visualization, image analysis, 3d image, image, microscopy, magnetic resonance, java, manifold viewer |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: Laboratory of Neuro Imaging |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
Free, Freely available | nif-0000-23318 | http://www.nitrc.org/projects/shiva | SCR_002690 | Synchronized Histological Image View Arc | 2026-02-14 02:00:26 | 0 | |||||
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SumsDB Resource Report Resource Website 10+ mentions |
SumsDB (RRID:SCR_002759) | SumsDB, WebCaret | data repository, storage service resource, data analysis service, analysis service resource, data or information resource, production service resource, atlas, service resource, image repository, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures | segmentation, volume, neuroimaging, brain, fmri, stereotaxic foci, stereotaxic coordinate, brain-mapping, foci, structural mri, mri, cerebral cortex, cerebellar cortex, afni brik, analyze, atlas, nifti, registration, rendering, spatial transformation, surface analysis, surface rendering, visualization, volume rendering, brain mapping, neuroanatomy |
is used by: NIF Data Federation is listed by: Biositemaps is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: re3data.org is related to: Computerized Anatomical Reconstruction and Editing Toolkit is related to: Integrated Manually Extracted Annotation has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
Mental disease, Neurological disorder, Normal | Human Brain Project ; NSF ; NCI ; NLM ; NASA ; National Partnership for Advanced Computational Infrastructure ; NIMH R01 MH60974-06 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00016, r3d100010169 | http://brainvis.wustl.edu/wiki/index.php/Sums:About http://www.nitrc.org/projects/sumsdb https://doi.org/10.17616/R3JC76 |
SCR_002759 | SumsDB WebCaret, SumsDB Database, Web Caret, WebCaret Online Visualization, Surface Management System Database and WebCaret Online Visualization, SumsDB and WebCaret, Sums database, SumsDB (Surface Management System Database) and WebCaret Online Visualization, Sums DB, SumsDB (Surface Management System Database) WebCaret Online Visualization, Surface Management System Database | 2026-02-14 02:00:19 | 13 | ||||
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FSL Resource Report Resource Website 1000+ mentions |
FSL (RRID:SCR_002823) | software resource, software library, software toolkit | Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas. | dti, brain, imaging, data, structural, mri, diffusion, function, preprocessing, analysis, statistical, tractography, atlas, neuroimaging, parameter, reconstruction, volumetric, segmentation, independent, component, temporal, transformation |
uses: Neuroimaging Data Model is used by: Spinal Cord Toolbox is used by: Functional Real-time Interactive Endogenous Neuromodulation and Decoding (FRIEND) is used by: XFSL: An FSL toolbox is used by: CMIND PY lists: SUSAN lists: FUGUE lists: Miscvis lists: BayCEST lists: ICA-PNM is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: Rodent Brain Extraction Tool is related to: Human Connectome Coordination Facility is related to: BASH4RfMRI is related to: DW-MRI registration in FSL is related to: FSL extensions is related to: Diffusion MRI of Traumatic Brain Injury is related to: Segmentation of Hippocampus Subfields is related to: masked ICA (mICA) Toolbox has parent organization: University of Oxford; Oxford; United Kingdom has plug in: Multivariate Exploratory Linear Optimized Decomposition into Independent Components has plug in: FMRI Expert Analysis Tool has plug in: FABBER has plug in: BASIL has plug in: VERBENA has plug in: Brain Extraction Tool has plug in: FMRIB's Automated Segmentation Tool has plug in: FMRIB’s Integrated Registration and Segmentation Tool has plug in: Harvard - Oxford Cortical Structural Atlas has plug in: FMRIB's Linear Image Registration Tool has plug in: FNIRT has plug in: FSLVBM has plug in: SIENA has plug in: SIENAX has plug in: Multimodal Image Segmentation Tool has plug in: Brain Intensity AbNormality Classification Algorithm has plug in: Multimodal Surface Matching has plug in: fsl_anat has plug in: FMRIB's Diffusion Toolbox has plug in: Tract Based Spatial Statistics has plug in: XTRACT has plug in: eddy has plug in: topup has plug in: eddyqc has plug in: randomise has plug in: PALM has plug in: fsl-cluster has plug in: FDR has plug in: DualRegression has plug in: FLOBS has plug in: FSLeyes has plug in: Fslutils has plug in: Atlasquery has plug in: MCFLIRT has plug in: POSSUM has plug in: FSL-MRS |
EPSRC ; MRC ; BBSRC ; GlaxoSmithKline ; Pfizer |
PMID:21979382 PMID:19059349 PMID:15501092 |
Free, Available for download, Freely available | nif-0000-00305, birnlex_2067, SCR_007368 | http://www.nitrc.org/projects/fsl http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ https://sources.debian.org/src/fsl/ |
SCR_002823 | , FMRIB Software Library, fMRIB Software Library, Functional Magnetic Resonance Imaging of the Brain Software Library | 2026-02-14 02:00:32 | 4685 | |||||
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studyforrest.org Resource Report Resource Website 10+ mentions |
studyforrest.org (RRID:SCR_003112) | studyforrest.org | image repository, data repository, storage service resource, service resource | An MRI data repository that holds a set of 7 Tesla images and behavioral metadata. Multi-faceted brain image archive with behavioral measurements. For each participant a number of different scans and auxiliary recordings have been obtained. In addition, several types of minimally preprocessed data are also provided. The full description of the data release is available in a dedicated publication. This project invites anyone to participate in a decentralized effort to explore the opportunities of open science in neuroimaging by documenting how much (scientific) value can be generated out of a single data release by publication of scientific findings derived from a dataset, algorithms and methods evaluated on this dataset, and/or extensions of this dataset by acquisition and integration of new data. | neuroimaging, open data, brain, brain scan, fmri, stimulus material, participant demographic, stimulus, demographic, experimental protocol, structure mri, mri, 7-tesla, data set, auditory system, language, perception |
uses: OpenNeuro uses: rsync uses: XNAT - The Extensible Neuroimaging Archive Toolkit is used by: NIF Data Federation is listed by: NITRC-IR is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Otto-von-Guericke University Magdeburg; Saxony-Anhalt; Germany |
BMBF 01GQ1112; BMBF 01GQ1411; NSF 1129855; DFG PO 548/15-1 |
Free, Available for download, Freely available | r3d100011071, nlx_156710 | http://www.nitrc.org/projects/studyforrest https://doi.org/10.17616/R3SW5S |
SCR_003112 | study forrest, studyforrest | 2026-02-14 02:00:39 | 34 | |||||
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brainmap.org Resource Report Resource Website 100+ mentions |
brainmap.org (RRID:SCR_003069) | BrainMap | data or information resource, software resource, database, software application | A community database of published functional and structural neuroimaging experiments with both metadata descriptions of experimental design and activation locations in the form of stereotactic coordinates (x,y,z) in Talairach or MNI space. BrainMap provides not only data for meta-analyses and data mining, but also distributes software and concepts for quantitative integration of neuroimaging data. The goal of BrainMap is to develop software and tools to share neuroimaging results and enable meta-analysis of studies of human brain function and structure in healthy and diseased subjects. It is a tool to rapidly retrieve and understand studies in specific research domains, such as language, memory, attention, reasoning, emotion, and perception, and to perform meta-analyses of like studies. Brainmap contains the following software: # Sleuth: database searches and Talairach coordinate plotting (this application requires a username and password) # GingerALE: performs meta-analyses via the activation likelihood estimation (ALE) method; also converts coordinates between MNI and Talairach spaces using icbm2tal # Scribe: database entry of published functional neuroimaging papers with coordinate results | 3d model, atlas, data management, imaging, map, neuroinformatics, warping, neuroimaging, brain, talairach, mni, java, modeling, magnetic resonance, nifti-1, ontology, os independent, pet, spect, visualization, functional neuroimaging, fmri |
uses: Scribe is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Brede Database has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA is parent organization of: Sleuth is parent organization of: GingerALE |
Healthy, Diseased | NIMH 2R01-MH074457 | PMID:15897617 PMID:11967563 PMID:15846810 |
Free, Freely available | nif-0000-00049 | http://www.nitrc.org/projects/brainmap | SCR_003069 | BrainMap Database | 2026-02-14 02:00:29 | 448 | |||
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Brian Simulator Resource Report Resource Website 10+ mentions |
Brian Simulator (RRID:SCR_002998) | Brian | software resource, simulation software, software application | Software Python package for simulating spiking neural networks. Useful for neuroscientific modelling at systems level, and for teaching computational neuroscience. Intuitive and efficient neural simulator. | simulation, spiking, neuron, brain, communication, modelling, computational neuroscience, python, spiking neuron, neural network |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Ecole Normale Superieure; Paris; France |
European Union ; French National Research Agency ; CNRS ; Ecole Normale Superieure; Paris; France |
DOI:10.7554/eLife.47314 DOI:10.3389/neuro.01.026.2009 DOI:10.7554/eLife.47314 |
Free, Available for download, Freely available | nif-0000-30223 | http://www.nitrc.org/projects/brian | SCR_002998 | Brian 2, Brian spiking neural network simulator, Brian2 | 2026-02-14 02:00:28 | 26 | ||||
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Open Connectome Project Resource Report Resource Website 1+ mentions |
Open Connectome Project (RRID:SCR_004232) | Open Connectome Project | data repository, storage service resource, web service, data analysis service, image repository, analysis service resource, data set, data or information resource, production service resource, source code, service resource, data access protocol, software 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 | 2026-02-14 02:00:57 | 7 | ||||
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Open Science Framework Resource Report Resource Website 500+ mentions |
Open Science Framework (RRID:SCR_003238) | OSF | data repository, storage service resource, 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 | 2026-02-14 02:00:24 | 741 |
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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.
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