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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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ChIPseeqer Resource Report Resource Website 10+ mentions |
ChIPseeqer (RRID:SCR_001545) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software that provides a comprehensive framework for the analysis of ChIP-seq data. | sequence analysis, framework, ChIP, chip-seq, chip-seq data, sequencing, data, algorithm |
is listed by: OMICtools has parent organization: Weill Cornell Medical College; New York; USA |
DOI:10.1186/1471-2105-12-277 | Free, Available for download, Freely available | OMICS_00422 | SCR_001545 | 2026-08-04 09:40:24 | 18 | ||||||||
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eBioNews - A Subsidiary of eBioCenter Resource Report Resource Website |
eBioNews - A Subsidiary of eBioCenter (RRID:SCR_001717) | topical portal, portal, data or information resource | eBioNews specializes in online information services and resource exchanges in the fields of life sciences and biotechnology. By applying its knowledge database and content management system (CMS), eBioNews offers readers and customers the organized and comprehensive information. eBioNews also provides a membership-based service to assist our customers in information and data search, processing, storage, and sharing. Generally, eBioNews covers the following areas: - life science frontiers - news and discussions - features and specials - resources and sourcing - career development - academic and industry - training and education Additionally, eBioNews information is organized into the following two clusters: - News Center: 1. Headlights 2. Research Frontiers 3. General Research 4. Clinical Development 5. Enterprise & Industry 6. Products & Services 7. Investment & Financials 8. Features 9. Newsletter The News Center consists of the elements and mechanisms that enable collecting, organizing, displaying, and delivering life science related information, data, and knowledge. - Resource Center: 1. eBioResources 2. Cooperation 3. Events 4. Human Resources 5. Intellectual Property 6. Finance & Legal 7. Operations 8. Organization 9. Publication The Resource Center is a system that hosts and facilitates the resource-related information between and among multiple parties, especially for promoting cooperation, collaboration, consortium, partnering, joint venture, licensing, out-sourcing, and trading. Sponsors: This resource is supported by eBioCenter Corporation. | education, biology, biotechnology, career, data, database, developing, industry, knowledge, life, life science, mechanism, news, organizing, processing, science, service, sharing, storage, training | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10216 | http://www.ebionews.com/ | SCR_001717 | eBioNews | 2026-08-04 09:40:27 | 0 | ||||||||
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Brainstorm Resource Report Resource Website 500+ mentions |
Brainstorm (RRID:SCR_001761) | Brainstorm | data processing software, data analysis software, software resource, software application, data visualization software | Software as collaborative, open source application dedicated to analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology. User-Friendly Application for MEG/EEG Analysis. | MEG, EEG, data, magnetoencephalography, electroencephalography, visualization, processing, analysis, brain, recording, fNIRS, ECoG, electrophysiology |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: OpenMEEG is related to: Open MEG Archive is related to: MATLAB has parent organization: University of Southern California; Los Angeles; USA |
NIBIB R01 EB002010; NIBIB R01 EB009048; NIBIB R01 EB000473; NIBIB R01 EB026299; CNRS ; McGill University |
PMID:21584256 | Free, Available for download, Freely available | nif-0000-10267 | http://www.nitrc.org/projects/bst, https://github.com/brainstorm-tools/brainstorm3 | SCR_001761 | brainstorm3 | 2026-08-04 09:40:28 | 558 | ||||
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ITK-SNAP Resource Report Resource Website 1000+ mentions |
ITK-SNAP (RRID:SCR_002010) | segmentation software, data processing software, software resource, software application, image analysis software | Open source interactive software application for three dimentional medical images, manual delineation of anatomical regions of interest, and performing automatic image segmentation. Used for delineating anatomical structures and regions in MRI, CT and other 3D biomedical imaging data.WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons). | medical, image, segmentation, delineating, anatomical, structure, region, MRI, CT, 3D image, data |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: neurodebian is related to: AHEAD is related to: LiverSegm is related to: Waxholm Space Atlas of the Sprague Dawley Rat Brain is related to: Waxholm Space has parent organization: University of Pennsylvania; Philadelphia; USA |
NIBIB R01 EB014346 | PMID:29946897 | Free, Available for download, Freely available | nif-0000-00317 | https://github.com/google/neuroglancer, https://opensource.google.com/projects/neuroglancer | SCR_002010 | 2026-08-04 09:40:32 | 2629 | ||||||
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NIDA Data Share Resource Report Resource Website 10+ mentions |
NIDA Data Share (RRID:SCR_002002) | database, storage service resource, data repository, service resource, catalog, data or information resource | Website which allows data from completed clinical trials to be distributed to investigators and public. Researchers can download de-identified data from completed NIDA clinical trial studies to conduct analyses that improve quality of drug abuse treatment. Incorporates data from Division of Therapeutics and Medical Consequences and Center for Clinical Trials Network. | drug of abuse, clinical, data, data sharing, human, clinical trial, experimental protocol, addiction, drug, addiction, data set, substance abuse |
is used by: NIF Data Federation is used by: Integrated Datasets is used by: NIH Heal Project is recommended by: National Library of Medicine is recommended by: BRAIN Initiative is listed by: re3data.org is related to: NIDA Networking Project: Facilitating information exchange and research collaboration is related to: Integrated Manually Extracted Annotation has parent organization: National Drug Abuse Treatment Clinical Trials Network |
NIDA | Restricted | nif-0000-21981 | http://www.ctndatashare.org/ | SCR_002002 | NIDA Clinical Trials Data Share, CTN database, CTN Data Share, NIDA CTN Data Share | 2026-08-04 09:40:31 | 18 | ||||||
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The Immunology Database and Analysis Portal (ImmPort) Resource Report Resource Website 500+ mentions |
The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) | ImmPort | portal, topical portal, storage service resource, disease-related portal, controlled vocabulary, data repository, service resource, ontology, database, data or information resource | Data sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology. | immunology, basic, clinical, data, share, store, analyze, exchange, dataset, immune, mediated, disease, analysis, tool, FASEB list |
is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NIDDK Research Resources is affiliated with: Cytokine Registry is related to: MetaCyto is related to: The 10000 Immunomes is related to: NIAID |
Immune mediated disease | NIH ; NIAID ; DAIT ; NIAID HHSN266200400076C; NIAID HHSN272201200028C |
PMID:24791905 | nlx_152691, r3d100012529 | http://www.immport.org/immport-open/public/home/home, http://www.immport.org/ | http://www.immport.org | SCR_012804 | Immunology Data and Analysis Portal, ImmPort system, ImmPort, Immunology Database and Analysis Portal | 2026-08-04 09:43:05 | 987 | |||
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eQTL Visualization Tool Resource Report Resource Website 1+ mentions |
eQTL Visualization Tool (RRID:SCR_013413) | data processing software, data visualization software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. eQTL Explorer was developed as a computational resource to visualize and explore data from combined genome-wide expression and linkage studies is essential for the development of testable hypotheses. This visualization tool stores expression profiles, linkage data and information from external sources in a relational database and enables simultaneous visualization and intuitive interpretation of the combined data via a Java graphical interface. eQTL Explorer also provides a new and powerful tool to interrogate these very large and complex datasets. eQTLexplorer allows users to mine and understand data from a repository of genetical genomics experiments. It will graphically display eQTL information based on a certain number of selection criteria, including: tissue type, p-value, cis/trans, probeset Affymetrix id and PQTL type. Sponsors: This work was funded by the MRC Clinical Sciences Centre and the Wellcome Trust programme for Cardiovascular Functional Genomics. | experiment, explore, expression, genome, genetic, genetical, cis, computational, data, database, genomic, grafical, interface, linkage, mine, pqtl type, p-value, repository, tissue, tissue type, trans, visualization, visualize | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10222 | SCR_013413 | eQTLexplorer | 2026-08-04 09:43:12 | 1 | |||||||||
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HED Tags Resource Report Resource Website 1+ mentions |
HED Tags (RRID:SCR_014074) | HED | narrative resource, standard specification, data or information resource | Strategy guide for HED Annotation. Framework for systematically describing laboratory and real world events.HED tags are comma separated path strings. Organized in forest of groups with roots Event, Item, Sensory presentation, Attribute, Action, Participant, Experiment context, and Paradigm. Used for preparing brain imaging data for automated analysis and meta analysis. Applied to brain imaging EEG, MEG, fNIRS, multimodal mobile brain or body imaging, ECG, EMG, GSR, or behavioral data. Part of Brain Imaging Data Structure standard for brain imaging. | Data, structure, standard, EEG, brain, imaging, comma, separated, path, string, analysis, MEG, fNIRS, multimodal, ECG, EMG, GSR, behavioral, BRAIN Initiative |
is used by: NIMH Data Archive is used by: HeadIT is used by: OpenNeuro is recommended by: BRAIN Initiative has parent organization: University of California at San Diego; California; USA |
Swartz Foundation ; Army Research Laboratory Cooperative Agreement ; NIMH R01MH084819; NINDS R01 NS047293 |
PMID:27799907 | Free, Freely available | SCR_017630 | SCR_014074 | Hierarchical Event Descriptor Tags, Hierarchical Event Descriptor, HED, HED tags | 2026-08-04 09:43:19 | 7 | |||||
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Skyline Resource Report Resource Website 1000+ mentions |
Skyline (RRID:SCR_014080) | data processing software, software application, software resource, data analysis software | Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences. | Proteomics, SRM, MRM, DDA, DIA, shotgun, mass, spectrometry, data, analysis, quantitative |
uses: MSstats is related to: ProteoWizard has parent organization: University of Washington; Seattle; USA works with: PanoramaWeb |
NCI U24 CA126479; NIDDK R01 DK069386; NCRR P41 RR011823; NIA P30 AG013280; NHLBI R01 HL082747 |
PMID:20147306 | Free, Available for download, Freely available | SCR_014080 | 2026-08-04 09:43:20 | 2805 | ||||||||
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Origin Resource Report Resource Website 10000+ mentions |
Origin (RRID:SCR_014212) | data processing software, data analysis software, software resource, software application, data visualization software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 4, 2025.Software application for data analysis and graphing. Origin contains a variety of different graph types, including statistical plots, 2D and 3D vector graphs, and counter graphs. More advance version is OriginPro which offers advanced analysis tools and Apps for Peak Fitting, Surface Fitting, Statistics and Signal Processing. | data, analysis, software, authoring, tool, scripting, graphing, statistical, publication |
is listed by: SoftCite is related to: OriginPro |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015636 | https://www.originlab.com/index.aspx?go=PRODUCTS&PID=1834 | SCR_014212 | OriginPro | 2026-08-04 09:43:22 | 13956 | |||||||
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FactoMineR Resource Report Resource Website 1000+ mentions |
FactoMineR (RRID:SCR_014602) | data processing software, software application, software resource, data analysis software | Software R package for multivariate analysis which takes into account different types of data structure. Data can be organized in groups of variable, groups of individuals, or into hierarchy of variables. | multivariate, analysis, data, structure, organized, group, variable, individual, hierarchy |
is used by: ClustVis is listed by: CRAN |
https://cran.r-project.org/web/packages/FactoMineR/index.html, https://github.com/husson/FactoMineR | SCR_014602 | factominer | 2026-08-04 09:43:30 | 2349 | |||||||||
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TIDA Resource Report Resource Website 50+ mentions |
TIDA (RRID:SCR_014582) | data processing software, software application, software resource, data acquisition software | A software which is used to acquire physiological data from the HEKA Patch Clamp Amplifiers and HEKA interfaces. | data acquisition, heka, patch clamp, heka interface, physiological, data, acquisition software | Open source, Paired with a commercial product | SCR_014582 | 2026-08-04 09:43:28 | 96 | |||||||||||
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National Survey on Drug Use and Health Resource Report Resource Website 1+ mentions |
National Survey on Drug Use and Health (RRID:SCR_007031) | NSDUH, NSDUH/NHSDA, NHSDA, NSDUH / NHSDA | topical portal, portal, data set, data or information resource | NSDUH is the primary source of statistical information on the use of illegal drugs, alcohol, and tobacco by the U.S. civilian, noninstitutionalized population aged 12 or older. Conducted by the Federal Government since 1971, the survey collects data through face-to-face interviews with a representative sample of the population at the respondent''s place of residence. Correlates in OAS reports include the following: age, gender, pregnancy status, race / ethnicity, education, employment, geographic area, frequency of use, and association with alcohol, tobacco, & illegal drug use. NSDUH collects information from residents of households and noninstitutional group quarters (e.g., shelters, rooming houses, dormitories) and from civilians living on military bases. The survey excludes homeless persons who do not use shelters, military personnel on active duty, and residents of institutional group quarters, such as jails and hospitals. Most of the questions are administered with audio computer-assisted self-interviewing (ACASI). ACASI is designed to provide the respondent with a highly private and confidential mode for responding to questions in order to increase the level of honest reporting of illicit drug use and other sensitive behaviors. Less sensitive items are administered by interviewers using computer-assisted personal interviewing (CAPI). The 2010 NSDUH employed a State-based design with an independent, multistage area probability sample within each State and the District of Columbia. The eight States with the largest population (which together account for about half of the total U.S. population aged 12 or older) were designated as large sample States (California, Florida, Illinois, Michigan, New York, Ohio, Pennsylvania, and Texas) and had a sample size of about 3,600 each. For the remaining 42 States and the District of Columbia, the sample size was about 900 per State. The design oversampled youths and young adults; each State''s sample was approximately equally distributed among three age groups: 12 to 17 years, 18 to 25 years, and 26 years or older. | substance abuse, data, clinical, mental health, marijuana, cocaine, heroin, hallucinogen, inhalant, psychotherapeutic, alcohol, tobacco, illicit drug, adolescent, early adult, adult | has parent organization: RTI International | Drug Abuse | US Department of Health and Human Services HHSS283200800004C | Public | nlx_146277 | SCR_007031 | National Household Survey on Drug Abuse, SAMHSA National Survey on Drug Use & Health, National Survey on Drug Use Health, National Survey on Drug Use & Health | 2026-08-04 09:41:45 | 2 | |||||
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Physiobank Resource Report Resource Website 10+ mentions |
Physiobank (RRID:SCR_006949) | PhysioBank | database, storage service resource, data repository, service resource, catalog, data or information resource | Archive of well-characterized digital recordings of physiologic signals and related data for use by the biomedical research community. PhysioBank currently includes databases of multi-parameter cardiopulmonary, neural, and other biomedical signals from healthy subjects and patients with a variety of conditions with major public health implications, including sudden cardiac death, congestive heart failure, epilepsy, gait disorders, sleep apnea, and aging. The PhysioBank Archives now contain over 700 gigabytes of data that may be freely downloaded. PhysioNet is seeking contributions of data sets that can be made freely available in PhysioBank. Contributions of digitized and anonymized (deidentified) physiologic signals and time series of all types are welcome. If you have a data set that may be suitable, please review PhysioNet''s guidelines for contributors and contact them. | physiologic, signal, data, biomedical, research, community, cardiopulmonary, neural, biomedical, health, cardiac, death, congestive heart failure, epilepsy, gait, disorder, sleep apnea, bibliographic, normal, physiologic signal, time series, FASEB list |
is used by: NIF Data Federation is used by: Integrated Datasets is related to: PhysioToolkit is parent organization of: Gait in Aging and Disease Database is parent organization of: Gait in Parkinson's Disease is parent organization of: Gait Dynamics in Neuro-Degenerative Disease Data Base is parent organization of: Noise Enhancement of Sensorimotor Function |
Healthy, Sudden cardiac death, Congestive heart failure, Epilepsy, Gait disorder, Sleep apnea, Aging | NIGMS ; NIBIB U01-EB-008577 |
PMID:10851218 | Free, The community can contribute to this resource, Acknowledgement requested | nlx_48903, r3d100011236 | https://doi.org/10.17616/R3J048 | SCR_006949 | 2026-08-04 09:41:43 | 39 | ||||
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ModelDB Resource Report Resource Website 100+ mentions |
ModelDB (RRID:SCR_007271) | ModelDB | storage service resource, data repository, service resource, database, data or information resource | Curated database of published models so that they can be openly accessed, downloaded, and tested to support computational neuroscience. Provides accessible location for storing and efficiently retrieving computational neuroscience models.Coupled with NeuronDB. Models can be coded in any language for any environment. Model code can be viewed before downloading and browsers can be set to auto-launch the models. The model source code has to be available from publicly accessible online repository or WWW site. Original source code is used to generate simulation results from which authors derived their published insights and conclusions. | repository, collection, network, neuron, computational, neuroscience, model, simulation, neural, data |
is used by: NIF Data Federation lists: ModelRun is listed by: 3DVC is listed by: Biositemaps is listed by: Integrated Models is related to: SimToolDB is related to: NeuronDB is related to: NeuronVisio is related to: Integrated Manually Extracted Annotation is related to: Allen Institute for Brain Science has parent organization: Yale University; Connecticut; USA works with: MicrocircuitDB |
NIMH ; NINDS ; NCI ; Human Brain Project ; NIDCD P01 DC004732; NIDCD R01 DC009977 |
PMID:15218350 PMID:15055399 PMID:8930855 |
Free, Freely available, Acknowledgement requested | nif-0000-00004, r3d100011330 | https://doi.org/10.17616/R3P61F | SCR_007271 | Model_DB, Model Database, Model DB, Model-DB | 2026-08-04 09:41:48 | 304 | ||||
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BioMANTA Resource Report Resource Website 1+ mentions |
BioMANTA (RRID:SCR_007177) | BioMANTA | portal, topical portal, software resource, disease-related portal, research forum portal, controlled vocabulary, ontology, data or information resource | This project encompasses development of novel biological network analysis methods and infrastructure for querying biological data in a semantically-enabled format, and aims to create a semantic interactome model. Research within the BioMANTA project will focus on computational modelling and analysis, primarily using Semantic Web technologies and Machine Learning methods, of large-scale protein-protein interaction and compound activity networks across a wide variety of species. A range of information such as kinetic activity, tissue expression, and subcellular localization and disease state attributes will be included in the resulting data model. Protein interactions are a fundamental component of biological processes. Many proteins are functional only in multimeric complexes, or require interaction partners to achieve their correct localisation or function. For this reason, the study of protein-protein interaction (PPI) networks has become an area of growing interest in computational biology. Through the use of Semantic Web technologies such as Resource Description Framework (RDF) and Web Ontology Language (OWL), interaction data is modelled to create a knowledge representation in which meaning is vested in the ontology rather than instances of data. Stochastic and computational intelligence methods are applied to this data to infer high coverage networks. Semantic inferencing is used to infer previously unknown and meaningful pathways. Major project components: - The BioMANTA Ontology:- An OWL DL ontology incorporating the PSI-MI Ontology, the NCBI Taxonomy, and elements of BioPax ontology and Gene Ontology (describing subcellular localisation). This allows us to re-use existing ontologies, thereby reducing overheads associated with knowledge acquisition in the ontology development process. We are able to integrate existing public data that contain annotation in these formats. - Data conversion & semantic protein integration:- A set of software components that convert protein-protein databases (DIP, MPact, IntAct, etc.) from PSI-MI XML to RDF compliant with the BioMANTA ontology. These software allow us to make these protein-protein interaction datasets (and more generally, any PSI-MI XML data) semantically available for querying and inference within BioMANTA. - A RDF triple store based on RDF Molecules and the MapReduce architecture:- A proof-of-concept RDF triple store using RDF molecules and Hadoop scale-out architectures. Regular RDF graphs are deconstructed into RDF molecules, which are distributed over distributed compute nodes in the MapReduce architecture, and are subsequently combined to form equivalent RDF graphs. Such an approach makes the distributed SPARQL querying and reasoning on RDF triple stores possible. - A quantitative framework to integrate networks extracted from independent data sources (gene expression, subcellular localization, and ortholog mapping):- The model is multi-layer, with a first layer based on Decision Trees where each Decision tree is built on each dataset independently. The tree nodes are cut using Shannon''s entropy (mutual information); the decision of these independent trees is integrated using logistic regression, and the parameters are optimised using maximum likelihood. Sponsors: This resource is supported by the Pfizer Global Research and Development, the Institute for Molecular Bioscience (IMB), and the University of Queensland, Australia. | biological, network, model, analysis, semantic, interactome, biological, data, development, computational, process, protein, biology, ontology, knowledge, molecule, rdf, framework, subcellular, localization, gene, expression, ortholog, mapping, dataset | has parent organization: University of Queensland; Brisbane; Australia | nif-0000-30183 | SCR_007177 | The Modelling and Analysis of Biological Network Activity | 2026-08-04 09:41:46 | 2 | ||||||||
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Function BIRN Resource Report Resource Website 1+ mentions |
Function BIRN (RRID:SCR_007291) | FBIRN | topical portal, portal, data or information resource | The FBIRN Federated Informatics Research Environment (FIRE) includes tools and methods for multi-site functional neuroimaging. This includes resources for data collection, storage, sharing and management, tracking, and analysis of large fMRI datasets. fBIRN is a national initiative to advance biomedical research through data sharing and online collaboration. BIRN provides data-sharing infrastructure, software tools, strategies and advisory services - all from a single source. | fmri, 3d model, data storage, imaging, map, morphology, mri, neuroinformatics, segmentation, software, talairach, volume, warping, analyze, application, c++, csh/tcsh, data, database, database application, data resource, dicom, javascript, linux, magnetic resonance, nifti, ontology, pl/sql, posix/unix-like, python, quality metrics, spatial transformation, statistical operation, tcl/tk, unix shell, visualization, web resource, web service, workflow |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Biomedical Informatics Research Network is parent organization of: BXH/XCEDE Tools is parent organization of: FBIRN Image Processing Scripts |
NIGMS ; NCRR 1U24-RR025736; NCRR U24-RR021992; NCRR U24-RR021760; NCRR 1U24-RR026057-01 |
nif-0000-00070 | http://www.nitrc.org/projects/fbirn | http://nbirn.net/tools/browse_tools.shtm | SCR_007291 | Functional Imaging BIRN | 2026-08-04 09:41:49 | 2 | |||||
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Advanced 3D Visualization and Volume Modeling Resource Report Resource Website 1000+ mentions |
Advanced 3D Visualization and Volume Modeling (RRID:SCR_007353) | data processing software, data analysis software, software resource, software application, 3d visualization software, data visualization software | Software tool for visualizing, manipulating, and understanding data from tomography, microscopy, MRI and other imaging processes.Used to import and export options, to processes 3D image filtering and DTI based fiber tracking to visualization, volume and surface rendering, author tools for virtual reality navigation, video generation, and more. | 3d, data, visualization, tomography, imaging, process, MRI, microscopy, video | Commercially available | nif-0000-00262, SCR_014305 | http://www.amiravis.com | SCR_007353 | Amira, Amira 3D Software for Life Sciences, Amira 3D analysis | 2026-08-04 09:41:49 | 1629 | ||||||||
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Harvard Medical School, Department of Systems Biology: The Megason Lab -GoFigure Software Resource Report Resource Website 1+ mentions |
Harvard Medical School, Department of Systems Biology: The Megason Lab -GoFigure Software (RRID:SCR_008037) | portal, data processing software, topical portal, software resource, software application, data visualization software, data or information resource | GoFigure is a software platform for quantitating complex 4d in vivo microscopy based data in high-throughput at the level of the cell. A prime goal of GoFigure is the automatic segmentation of nuclei and cell membranes and in temporally tracking them across cell migration and division to create cell lineages. GoFigure v2.0 is a major new release of our software package for quantitative analysis of image data. The research focuses on analyzing cells in intact, whole zebrafish embryos using 4d (xyzt) imaging which tends to make automatic segmentation more difficult than with 2d or 2d+time imaging of cells in culture. This resource has developed an automatic segmentation pipeline that includes ICA based channel unmixing, membrane nuclear channel subtraction, Gaussian correlation, shape models, and level set based variational active contours. GoFigure was designed to meet the challenging requirements of in toto imaging. In toto imaging is a technology that we are developing in which we seek to track all the cell movements and divisions that form structures during embryonic development of zebrafish and to quantitate protein expression and localization on top of this digital lineage. For in toto imaging, GoFigure uses zebrafish embryos in which the nuclei and cell membranes have been marked with 2 different color fluorescent proteins to allow cells to be segmented and tracked. A transgenic line in a third color can be used to mark protein expression and localization using a genetic approach that this resource developed called FlipTraps or using traditional transgenic approaches. Embryos are imaged using confocal or 2-photon microscopy to capture high-resolution xyzt image sets used for cell tracking. The GoFigure GUI will provide many tools for visualization and analysis of bioimages. Since fully automatic segmentation of cells is never perfect, GoFigure will provide easy to use tools for semi-automatically and manually adding, deleting, and editing traces in 2d (figures-xy, xz, or yz), 3d (meshes- xyz), 4d (tracks- xyzt) and 4d+cell division (lineages). GoFigure will also provide a number of views into complex image data sets including 3d XYZ and XYT image views, tabular list views of traces, histograms, and scattergrams. Importantly, all these views will be linked together to allow the user to explore their data from multiple angles. Data will be easily sorted and color-coded in many ways to explore correlations in higher dimensional data. The GoFigure architecture is designed to allow additional segmentation, visualization, and analysis filters to be plugged in. Sponsors: GoFigure is developed by Harvard University., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | embryo, expression, fluorescent, gaussian, genetic, 2d, 2-photon, 4d, analysis, bioimage, cell, cell membrane, cell movement, channel, confocal, contour, culture, data, dimensional, high-resolution, histogram, in vivo, localization, microscopy, model, nuclear, nucleus, protein, scattergram, segmentation, shape, software, technology, toto imaging, tracking, transgenic, visualization, zebrafish, image | has parent organization: Harvard University; Cambridge; United States | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10243 | SCR_008037 | GoFigure | 2026-08-04 09:42:01 | 5 | ||||||||
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ConnectomeViewer: Multi-Modal Multi-Level Network Visualization and Analysis Resource Report Resource Website |
ConnectomeViewer: Multi-Modal Multi-Level Network Visualization and Analysis (RRID:SCR_008312) | ConnectomeViewer | data processing software, rendering software, d visualization software, data analysis software, software resource, software application, data visualization software, network analysis software, network graph visualization software | Extensible, scriptable, pythonic software tool for visualization and analysis in structural neuroimaging research on many spatial scales. Employing the Connectome File Format, diverse data such as networks, surfaces, volumes, tracks and metadata are handled and integrated. The field of Connectomics research benefits from recent advances in structural neuroimaging technologies on all spatial scales. The need for software tools to visualize and analyze the emerging data is urgent. The ConnectomeViewer application was developed to meet the needs of basic and clinical neuroscientists, as well as complex network scientists, providing an integrative, extensible platform to visualize and analyze Connectomics data. With the Connectome File Format, interlinking different datatypes such as hierarchical networks, surface data, volumetric data is easy and might provide new ways of analyzing and interacting with data. Furthermore, ConnectomeViewer readily integrates with: * ConnectomeWiki: a semantic knowledge base representing connectomics data at a mesoscale level across various species, allowing easy access to relevant literature and databases. * ConnectomeDatabase: a repository to store and disseminate Connectome files. | extensible, analysis, clinical, data, diverse, metadata, network, neuroscience, neuroscientist, pythonics, research, scriptable, software, structural, surface, technology, tool, track, visualization, volume, neuroimaging |
has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland has parent organization: University of Lausanne; Lausanne; Switzerland |
nif-0000-24442 | SCR_008312 | 2026-08-04 09:42:06 | 0 |
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If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
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If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
