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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Computer Integrated Systems for Microscopy and Manipulation Resource Report Resource Website 1+ mentions |
Computer Integrated Systems for Microscopy and Manipulation (RRID:SCR_001413) | CISMM | training resource | Biomedical technology research center that develops force technologies applicable over a wide range of biological settings, from the single molecule to the tissue, with integrated systems that orchestrate facile instrument control, multimodal imaging, and analysis through visualization and modeling. The Force Microscope Technologies Core designs instruments in an area of science where there are unusual opportunities: the measurement of forces and the integration with optical microscopy. Force technologies play the obvious role of both measuring events in the sample and modifying the sample during the experiment. It is through the microscope that the force data is correlated with simultaneous 3D optical images. The force technology development includes the magnetic bead technology in the 3D Force Microscope project, Atomic Force Microscopy in the nanoManipulator project, and Control Software to drive the instrumentation. This core is focused on providing the physical capability to perform the experiments and probe structure/property correlations. The Ideal User Interfaces core makes the connection between the user and the instrument, the model building, and the data. This includes control systems that allow the user to move the bead inside the cell culture with a handheld pen and the visualization techniques to view the optical microscope data as a rendered 3D image collocated with the force data. Using data to create, change, and understand a model is the focus of the Advanced Model Fitting and Analysis core. The quantitative reduction of images to structural, shape, and velocity parameters is the goal of Image Analysis. The immediate understanding of correlations across image fields and between data sets in the challenge of Visualization. The power of combining the strength of a computer science graphics group with a microscopy technology group is most evident in the Graphics Hardware Acceleration project, which seeks to harness the speed of graphics processors for microscope data analysis and simulation. The Advanced Technology core pushes the boundaries of the Human Computer Interface through the investigation of improved techniques for the interaction of users with virtual environments, the real time lighting of virtual settings, and the enabling of multi-person collaboration. These techniques are validated and evaluated through physiological measures in virtual environments effectiveness evaluation studies. | microscope, visual analytics, image analysis, biomedical, bioinstrumatics, scanning electron microscope, light microscope, microscopy | has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA | Thrombosis, Lung disease, Cancer | NIBIB 5-P41-EB002025 | Freely Available | nlx_152648 | http://cismm.cs.unc.edu/ | SCR_001413 | UNC Chapel Hill Computer Integrated Systems for Microscopy and Manipulation | 2026-08-01 12:01:51 | 8 | ||||
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Center for Biomedical OCT Research Resource Report Resource Website 1+ mentions |
Center for Biomedical OCT Research (RRID:SCR_001418) | CBORT | training resource | Biomedical technology research center that pioneers and provides access to microscopic imaging instruments for biologic and clinical research. Optical coherence tomography (OCT) has evolved over the last two decades to become a standard of care for diagnostic ophthalmic imaging and is poised to make significant impact in the fields of cardiology and gastrointestinal endoscopy. Access to state-of-the-art instrumentation, however, has been limited to a relatively few research laboratories and the optimization of instruments for new biomedical applications has hindered the investigation of new opportunities. A major focus of CBORT will be to cultivate strategic research collaborations and respond to a pressing need for application-specific OCT instrumentation and hardware. | imaging, optical coherence tomography, microscope, catheter, endoscopy, near infrared fluorescence | has parent organization: Harvard Medical School; Massachusetts; USA | NIBIB P41EB015903 | Free, Freely Available | nlx_152640 | SCR_001418 | Center for Biomedical OCT Research and Translation | 2026-08-01 12:01:51 | 2 | ||||||
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BioMEMS Resource Center Resource Report Resource Website 1+ mentions |
BioMEMS Resource Center (RRID:SCR_001417) | BMRC | training resource | Biomedical technology research center that provides biomedical investigators with novel microsystems engineering tools for biological discovery, diagnostic, prognostic, and therapeutic applications. Thrust areas of interest are the development of novel living cell-based, lab-on-a-chip type devices for sorting blood cells, for high-throughput biochemistry in small volumes, and for studying cellular behavior in controlled microenvironments. | cell, tissue, microengineering, diagnostics, chip | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | NIBIB 5P41EB002503-12 | Free, Freely Available | nlx_152639 | SCR_001417 | Bio MicroElectroMechanical Systems (BioMEMS) Resource Center, Biomicroelectromechanical Systems (BioMEMS) Resource Center, BioMEMS, Bio MicroElectroMechanical Systems Resource Center | 2026-08-01 12:01:29 | 4 | ||||||
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NeuralAct Resource Report Resource Website 10+ mentions |
NeuralAct (RRID:SCR_002066) | NeuralAct | software resource | Software to visualize electrocorticographic (ECoG) and possibly also other kinds of neural activity (EEG / EMG/ DOT) on a 3D model of the cortical surface. The tool has been used to produce cortical activation images and image sequences in several recent studies using ECoG. The tool is written in matlab. The package is thoroughly documented and includes a demo. | brain, imaging, electrocorticographic, eeg, meg, dot, matlab, cortex, visualization, neural activity | NIH ; NIBIB EB006356; NIBIB EB000856; United States army research office W911NF-08-1-0216; United States army research office W911NF-07-1-0415 |
PMID:25381641 | Free, Available for download, Freely available | SciRes_000162 | http://www.neuralgate.org/software | SCR_002066 | NeuralAct: A tool to visualize cortical activity on a 3D model of the cortex | 2026-08-01 12:01:58 | 13 | |||||
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ENIGMA-DTI Pipeline Resource Report Resource Website 10+ mentions |
ENIGMA-DTI Pipeline (RRID:SCR_014649) | protocol | Pipeline which provides tools to extract whole-brain average and regional measurements from DTI images including FA, AD, RD and MD. Protocols for preprocessing, ENIGMA-DTI processing (skeletonization and ROI extraction), and GWAS analysis are available. Software tools used for each process are listed within the protocols. | dti, enigma, protocol, pipeline |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Southern California; Los Angeles; USA has parent organization: ENIGMA |
NIBIB U54 EB020403 | Available for download from NITRC | http://www.nitrc.org/projects/enigma_dti | SCR_014649 | ENIGMA-DTI protocol, ENIGMA DTI pipeline, ENIGMA DTI protocol | 2026-08-01 12:05:06 | 47 | |||||||
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TARGETgene Resource Report Resource Website 1+ mentions |
TARGETgene (RRID:SCR_001392) | TARGETgene | software resource, software application | MATLAB tool to effectively identify potential therapeutic targets and drugs in cancer using genetic network-based approaches. It can rapidly extract genetic interactions from a precompiled database stored as a MATLAB MAT-file without the need to interrogate remote SQL databases. Millions of interactions involving thousands of candidate genes can be mapped to the genetic network within minutes. While TARGETgene is currently based on the gene network reported in (Wu et al.,Bioinformatics 26:807-813, 2010), it can be easily extended to allow the optional use of other developed gene networks. The simple graphical user interface also enables rapid, intuitive mapping and analysis of therapeutic targets at the systems level. By mapping predictions to drug-target information, TARGETgene may be used as an initial drug screening tool that identifies compounds for further evaluation. In addition, TARGETgene is expected to be applicable to identify potential therapeutic targets for any type or subtype of cancers, even those rare cancers that are not genetically recognized. Identification of Potential Therapeutic Targets * Prioritize potential therapeutic targets from thousands of candidate genes generated from high-throughput experiments using network-based metrics * Validate predictions (prioritization) using user-defined benchmark genes and curated cancer genes * Explore biologic information of selected targets through external databases (e.g., NCBI Entrez Gene) and gene function enrichment analysis Initial Drug Screening * Identify for further evaluation existing drugs and compounds that may act on the potential therapeutic targets identified by TARGETgene * Explore general information on identified drugs of interest through several external links Operating System: Windows XP / Vista / 7 | disease target, drug discovery, drug, matlab, gene network, genetic interaction, gene, drug screening, mutation driver, therapeutic target, drug candidate, compound, mapping, analysis | has parent organization: Biomedical Simulations Resource | Cancer | NIBIB P41-EB001978 | PMID:22952662 | Free, Under the terms of a Release Agreement., Please cite | nlx_152573 | http://bmsr.usc.edu/Software/TARGET/TARGET.html | SCR_001392 | 2026-08-01 12:10:36 | 7 | ||||
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SCORE Resource Report Resource Website 100+ mentions |
SCORE (RRID:SCR_014165) | narrative resource, data or information resource, experimental protocol | A collection of methods for comparing the performance of different image algorithms. These methods generate quantitative scores that measure divergences to a standard. | experiment protocol, method, different image algorithm, quantitative score |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
NLM HHSN276201000584P; NIBIB 1R41 EB011796 |
SCR_014165 | 2026-08-02 09:06:27 | 458 | ||||||||||
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TumorSim Resource Report Resource Website 1+ mentions |
TumorSim (RRID:SCR_002604) | simulation software, software resource, software application | Simulation software that generates pathological ground truth from a healthy ground truth. The software requires an input directory that describes a healthy anatomy (anatomical probabilities, mesh, diffusion tensor image, etc) and then outputs simulation images. | clinical neuroinformatics, magnetic resonance, mri, brain, segmentation, simulation, tumor, ground truth |
uses: BrainWeb - Simulated Brain Database is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of Utah; Utah; USA |
Cancer | NIBIB R01 EB000219 | PMID:19119055 | Free, Available for download, Freely available | nlx_156007 | SCR_002604 | 2026-08-02 09:03:23 | 1 | ||||||
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NEURON Resource Report Resource Website 100+ mentions |
NEURON (RRID:SCR_017449) | simulation software, software resource, software application | Software for computational neurophysiology. Simulation environment is used for building and using computational models of neurons and networks of neurons. NEURON Users Group can participate in collaborative development of documentation, tutorials, and software. | Computational, neurophysiology, model, neuron, network, building, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: Yale University; Connecticut; USA |
NIBIB EB022903 | Free, Available for download, Freely available | https://github.com/neuronsimulator/nrn | SCR_017449 | 2026-08-02 09:07:32 | 241 | ||||||||
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Spectroscopic Imaging, VIsualization, and Computing (SIVIC) Resource Report Resource Website |
Spectroscopic Imaging, VIsualization, and Computing (SIVIC) (RRID:SCR_027875) | SIVIC | software resource, software application | Software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies. | DICOM MR Spectroscopy Workflows, data processing, data visualization, DICOM MR spectroscopy data, | NCI RO1 CA127612; NCI P01 CA11816; NIBIB P41EB013598 |
PMID:23970895 | Free, Available for download, Freely available | SCR_027875 | 2026-08-01 12:14:39 | 0 | ||||||||
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Center for Imaging of Neurodegenerative Diseases Resource Report Resource Website |
Center for Imaging of Neurodegenerative Diseases (RRID:SCR_001968) | CIND | organization portal, data or information resource, portal | Biomedical technology research center that develops and validates new imaging methods for detecting brain abnormalities in neurodegenerative diseases, including Alzheimer's disease, vascular dementia, frontotemporal dementia, Parkinson's disease, as well as epilepsy, depression, and other conditions associated with nerve loss in the brain. As people around the globe live longer, the impact of neurodegenerative diseases is expected to increase further with dire social and economical consequences for societies if no effective treatments are developed soon. The development at CIND is aimed to improve magnetic resonance imaging (MRI). The ultimate goal of the scientific program is to identify imaging markers that improve accuracy in diagnosing neurodegenerative diseases at early stages, achieve more reliable prognoses of disease progression, and facilitate the discovery of effective treatment interventions. In addition to addressing the general needs for studying neurodegenerative diseases, another focus of CIND concerns brain diseases associated with military service and war combat, such as post traumatic stress disorder (PTSD), brain trauma, gulf war illness and the long-term effects of these conditions on the mental health of veterans. The symbiosis between CIND and the Veterans Administration Medical Center in San Francisco makes this program uniquely suited to serve military veterans. | Biomedical Technology Research Center, depression, mri, imaging, neuroimaging | has parent organization: University of California at San Francisco; California; USA | Neurodegenerative disease, Alzheimer's disease, Vascular dementia, Frontotemporal dementia, Parkinson's disease, Epilepsy, Depressive Disorder, Post-Traumatic Stress Disorder, Brain injury, Gulf war illness | NIBIB | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10539 | http://www.cind.research.va.gov/index.asp | SCR_001968 | UCSF Center for Imaging of Neurodegenerative Diseases | 2026-08-02 09:03:26 | 0 | ||||
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Cambridge Brain Activation Resource Report Resource Website 10+ mentions |
Cambridge Brain Activation (RRID:SCR_007109) | CamBA | software toolkit, workflow software, software application, data processing software, image analysis software, software resource | 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 | 2026-08-03 09:33:16 | 11 | ||||||
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LONI Image and Data Archive Resource Report Resource Website 50+ mentions |
LONI Image and Data Archive (RRID:SCR_007283) | IDA, LONI IDA, | image collection, data or information resource, database | Archive used for archiving, searching, sharing, tracking and disseminating neuroimaging and related clinical data. IDA is utilized for dozens of neuroimaging research projects across North America and Europe and accommodates MRI, PET, MRA, DTI and other imaging modalities. | data storage, mri, pet, mra, dti, neuroimaging, image storage, histology, fmri, spect, normal, control, alzheimer's disease, mild cognitive impairment, data sharing, clinical, protection, brain, cryosection, FASEB list |
is recommended by: National Library of Medicine is listed by: NIH Data Sharing Repositories |
Control, Autism, Parkinson's disease, Alzheimer's disease, Mild Cognitive Impairment, Normal control, Aging | NIBIB | Restricted | nif-0000-00040, r3d100012840 | https://ida.loni.usc.edu/login.jsp?search=true, https://doi.org/10.17616/R39N6D | https://ida.loni.ucla.edu/login.jsp | SCR_007283 | , IDA, LONI Database, LONI, Image Data Archive | 2026-08-03 09:33:26 | 87 | |||
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Brain Architecture Management System Resource Report Resource Website 1+ mentions |
Brain Architecture Management System (RRID:SCR_007251) | BAMS | data repository, ontology, service resource, database, storage service resource, controlled vocabulary, data or information resource | Knowledge management system designed to handle neurobiological information at different levels of organization of vertebrate nervous system. Database and repository for information about neural circuitry, storing and analyzing data concerned with nomenclature, taxonomy, axonal connections, and neuronal cell types. Handles data and metadata collated from original literature, or inserted by scientists that is associated to four levels of organization of vertebrate nervous system. Data about expressed molecules, neuron types and classes, brain regions, and networks of brain regions. | neurobiology, vertebrate, nervous, system, database, repository, neural, circuitry, analysis, data, nomenclature, taxonomy, axonal, connection, cell, |
is used by: NIF Data Federation is used by: Integrated Nervous System Connectivity is related to: Integrated Manually Extracted Annotation has parent organization: University of Southern California; Los Angeles; USA is parent organization of: BAMS Nested Regions is parent organization of: BAMS Connectivity is parent organization of: BAMS Cells is parent organization of: BAMS Neuroanatomical Ontology |
NIBIB ; Human Brain Project ; NIMH MH61223; NINDS NS16686; NINDS NS50792 |
Restricted | nif-0000-00018 | http://brancusi.usc.edu/bkms/ | SCR_007251 | Brain Architecture Management System, The Brain Architecture Management System | 2026-08-03 09:33:19 | 6 | |||||
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NSR Physiome Project Resource Report Resource Website 1+ mentions |
NSR Physiome Project (RRID:SCR_007379) | NSR Physiome Project | portal, professional program, software application, topical portal, simulation software, data or information resource, software resource, training resource | Database of physiological, pharmacological, and pathological information on humans and other organisms and integration through computational modeling. Models include everything from diagrammatic schema, suggesting relationships among elements composing a system, to fully quantitative, computational models describing the behavior of physiological systems and an organism''s response to environmental change. Each mathematical model is an internally self-consistent summary of available information, and thereby defines a working hypothesis about how a system operates. Predictions from such models are subject to test, with new results leading to new models.BR /> A Tool developed for the NSR Physiome project is JSim, an open source, free software. JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim''s primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains. JSim models may intermix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. JSim''s model compiler can automatically insert conversion factors for compatible physical units as well as detect and reject unit unbalanced equations. JSim also imports the SBML and CellML model archival formats. All JSim models are open source. Goals of the Physiome Project: - To develop and database observations of physiological phenomenon and interpret these in terms of mechanism (a fundamentally reductionist goal). - To integrate experimental information into quantitative descriptions of the functioning of humans and other organisms (modern integrative biology glued together via modeling). - To disseminate experimental data and integrative models for teaching and research. - To foster collaboration amongst investigators worldwide, to speed up the discovery of how biological systems work. - To determine the most effective targets (molecules or systems) for therapy, either pharmaceutic or genomic. - To provide information for the design of tissue-engineered, biocompatible implants. | physiome, computational modeling, cell, organ, organism, human, model, physiological, pharmacological, pathological, model repository, sbml, cellml, biophysics, biochemistry, database, proteome, jsim simulation analysis system, data analysis tool, parameter optimization tool, integrating biological system | has parent organization: University of Washington; Seattle; USA | NSF BE08407; NHLBI T15 HL88516-01; NSF BES-0506477; NHLBI R01HL073598; NIBIB R01EB001973 |
nif-0000-00532 | SCR_007379 | National Simulation Resource Physiome Project | 2026-08-03 09:33:27 | 3 | |||||||
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jViewbox Resource Report Resource Website |
jViewbox (RRID:SCR_008274) | image processing software, software resource, software application, data processing software | A portable software framework for medical imaging research. jViewbox consists of a set of Java classes organized under a simple but extensive API that provides the core functionality of 2D image presentation needed by most imaging applications. It follows Java's Swing model closely to make it easy for application developers to build GUIs where end users can use various tools in a tool bar to manipulate the image displays. No optional add-ons or native code is used, which makes jViewBox compatible with any standard Java 2 Runtime Environment (version 1.3 or later). | imaging, magnetic resonance imaging, image processing software |
is related to: Laboratory of Neuro Imaging has parent organization: University of Southern California; Los Angeles; USA |
NIBIB 9P41EB015922-15; NCRR 2-P41-RR-013642-15 |
Available for educational and research purposes only | nif-0000-23317 | SCR_008274 | 2026-08-03 09:34:01 | 0 | ||||||||
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BrainInfo Resource Report Resource Website 10+ mentions |
BrainInfo (RRID:SCR_003142) | portal, standard specification, database, narrative resource, topical portal, atlas, data or information resource | Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures. | brain, neuroanatomy |
is used by: NIF Data Federation is listed by: Biositemaps is related to: INIA19 Primate Brain Atlas has parent organization: University of Washington; Seattle; USA has parent organization: University of California at San Diego; California; USA |
The Human Brain Project ; NIBIB ; NLM LM/OD-06243; NIH Office of the Director LM/OD-06243; NIMH MHO69259; NCRR RR-00166 |
PMID:21789500 PMID:21163300 PMID:18368361 PMID:15055392 |
Free, Freely available | nif-0000-00019 | SCR_003142 | Brain Info | 2026-08-03 09:32:12 | 16 | ||||||
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Open Connectome Project Resource Report Resource Website 1+ mentions |
Open Connectome Project (RRID:SCR_004232) | Open Connectome Project | data repository, production service resource, data analysis service, web service, service resource, image repository, source code, storage service resource, analysis service resource, data access protocol, data or information resource, software resource, data set | 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 | 2026-08-03 09:32:23 | 7 | ||||
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Viking Viewer for Connectomics Resource Report Resource Website 10+ mentions |
Viking Viewer for Connectomics (RRID:SCR_005986) | data management software, software application, data processing software, collaboration tool, software resource | A web-compliant application that allows connectomics visualization by converting datasets to web-optimized tiles, delivering volume transforms to client devices, and providing groups of users with connectome annotation tools and data simultaneously via conventional internet connections. Viking is an extensible tool for connectomics analysis and is generalizable to histomics applications. | annotation, 2d image, microscopy image, volume, serial section, 3d reconstruction, segmentation, microscopy, visualization, optical imaging, connectomics, synapse, retina, brain |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: 3DVC has parent organization: University of Utah; Utah; USA |
Research to Prevent Blindness ; University of Utah; Utah; USA ; Graduate Research Fellowship ; Utah Science Technology and Research Initiative ; NEI R01 EY02576; NEI R01 EY015128; NEI P01 EY014800; NSF 0941717; NIDCD T32DC008553; NIBIB EB005832 |
PMID:21118201 | Open source | nlx_151360 | http://www.nitrc.org/projects/viking_viewer | SCR_005986 | Viking, Viking Connectome Annotation System, Viking Annotation System | 2026-08-03 09:32:58 | 14 | |||||
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Ligand Expo Resource Report Resource Website |
Ligand Expo (RRID:SCR_006636) | resource, data or information resource, database | An integrated data resource for finding chemical and structural information about small molecules bound to proteins and nucleic acids within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry. A sketch tool is also provided for building new chemical definitions from reported PDB chemical components. | element, fingerprint, formula, amino acid, aromatic ring, atom, bound, carbon, chemical, component, depot, ligand, molecular, molecule, nitrogen, nucleic acid, nucleotide, pharmaceutical, protein, small molecule, structure, macromolecule, model |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: Worldwide Protein Data Bank (wwPDB) has parent organization: Rutgers University; New Jersey; USA has parent organization: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
NSF ; NIGMS ; DOE ; NLM ; NCI ; NCRR ; NIBIB ; NINDS ; NIDDK |
PMID:15059838 | nif-0000-21237, OMICS_02751 | http://ligand-depot.rutgers.edu/ | SCR_006636 | Ligand Depot | 2026-08-03 09:33:06 | 0 |
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