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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Sep 14, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
TADS - Treatment for Adolescents with Depression StudyResource, disease-related portal, topical portal, research forum portal, portal, clinical trial, data or information resourceA multi-site clinical research study examining the short- and long-term effectiveness of an antidepressant medication and psychotherapy alone and in combination for treating depression in adolescents ages 12 to 17. For teens treated in TADS, the trial is designed to provide best-practice practical care for depression. It is our hope that the overall study results will improve the future care of adolescents with depression. This study has been completed. TADS is designed to compare the effectiveness of established treatments for teenagers suffering from major depressive disorder (MDD). The treatments are: psychotherapy (talking therapy); medication; and the combination of psychotherapy and medication. Altogether, 432 teenagers (both males and females) ages 12 to 17, will take part in this study at 12 sites in the United States. The TADS design will provide answers to the following questions: What is the long-term effectiveness of medication treatment of teenagers who have major depression? What is the long-term effectiveness of a specific psychotherapy (talking therapy) in the treatment of teenagers who have major depression? How does medication treatment compare with psychotherapy in terms of effectiveness, tolerability and teenager and family acceptance? And, What is the cost-effectiveness of medication, psychotherapy and combined treatments? The medication being used in this study is called fluoxetine. Fluoxetine is also known as Prozac. Research has shown that medications like Prozac help depression in young persons. Fluoxetine has been approved by the FDA for use in the treatment of child and adolescent (ages 7 to 17 years) depression. The psychotherapy or talking therapy being used in this study is called Cognitive Behavioral Therapy (CBT). CBT is a talking therapy that will teach both the teenager and his or her family member (e.g., parent) new skills to cope better with depression. Specific topics include education about depression and the causes of depression, setting goals, monitoring mood, increasing pleasant activities, social problem-solving, correcting negative thinking, negotiation, compromise and assertiveness. CBT sessions may also help with resolving disagreements as they affect families. For more information see, http://www.clinicaltrials.gov/ct/show/NCT00006286?order=1 and http://www.nimh.nih.gov/trials/practical/tads/index.shtmlclinical trial, adolescent, major depressive disorder, depressive disorder, cognitive behavioral therapy, psychotherapy, drug, fluoxetine, nct00006286, young humanSCR_000037(TADS - Treatment for Adolescents with Depression Study, RRID:SCR_000037) ClinicalTrials.gov , Duke University School of Medicine; North Carolina; USA Major Depressive Disorder, Depressive DisorderNIMHused by: Limited Access Datasets From NIMH Clinical TrialsLast checked downnlx_146236
BAMS Nested RegionsResource, data or information resource, databaseBAMS is an online resource for information about neural circuitry. The BAMS Nested Regions view focuses on the major brain regions and their relationships. THIS RESOURCE IS NO LONGER AVAILABLE. Documented on July 7th, 2019.neural circuitry, brain region, brainSCR_000238(BAMS Nested Regions, RRID:SCR_000238)Brain Architecture Management System NIMH, NINDS, NINDS/NIMH/NIBIBused by: NIF Data FederationLast checked downnif-0000-10175
LORIS - Longitudinal Online Research and Imaging SystemResource, software resource, software application, data management softwareA modular and extensible web-based data management system that integrates all aspects of a multi-center study, from heterogeneous data acquisition to storage, processing and ultimately dissemination, within a streamlined platform. Through a standard web browser, users are able to perform a wide variety of tasks, such as data entry, 3D image visualization and data querying. LORIS also stores data independently from any image processing pipeline, such that data can be processed by external image analysis software tools. LORIS provides a secure web-based and database-driven infrastructure to automate the flow of clinical data for complex multi-site neuroimaging trials and studies providing researchers with the ability to easily store, link, and access significant quantities of both scalar (clinical, psychological, genomic) and multi-dimensional (imaging) data. LORIS can collect behavioral, neurological, and imaging data, including anatomical and functional 3D/4D MRI models, atlases and maps. LORIS also functions as a project monitoring and auditing platform to oversee data acquisition across multiple study sites. Confidentiality during multi-site data sharing is provided by the Subject Profile Management System, which can perform automatic removal of confidential personal information and multiple real-time quality control checks. Additionally, web interactions with the LORIS portal take place over an encrypted channel via SSL, ensuring data security. Additional features such as Double Data Entry and Statistics and Data Query GUI are included.neuroimaging, multi center, data querying, imaging data, platform, computed tomography, neuroinformatics, 3d, 4d, neurological, imaging, mri model, atlas, map, clinical, image processingSCR_000590(LORIS - Longitudinal Online Research and Imaging System, RRID:SCR_000590)McGill University; Montreal; Canada NICHD, NIMH, NINDSlisted by: NeuroImaging Tools and Resources Collaboratory (NITRC)PMID:22319489Last checked downnlx_144608http://www.nitrc.org/projects/loris
NVMResource, software resource, software application, data analysis software, data processing software, data visualization softwareSoftware tool for quantitative neuroanatomical measurements in volumetric image data. Used to draw regions of interest for subsequent fMRI analysis.quantitative, neuroanatomical, measurement, volumetric, image, data, draw, region, fMRI, analysis, morphologySCR_000600(NVM, RRID:SCR_000600)Neuromorphometrics NIMHlisted by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked downnlx_149080http://www.nitrc.org/projects/nvm
LONI Visualization ToolResource, data visualization software, software application, data processing software, software resourceA versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. It reads Analyze, Raw-binary and NetCDF volumetric data, as well as, Multi-Contour Files (MCF), LWO/LWS surfaces, atlas hierarchical brain-region labelings ( Brain Trees). It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture. LONI_Viz allows the user to interactively overlay and browse through several data volumes, zoom in and out in the axial, sagittal and coronal views, and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest, e.g., sulcal curves, on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest. The 3D features of the package include a SurfaceViewer and a full real-time VolumeRenderer. These allow the user to view the relative positions of different anatomical or functional regions which are not co-planar in any of the axial, sagittal or coronal 2D projection planes. The interactive part of LONI_Viz features a region drawing module used for manual delineation of regions of interest. A series of 2D contours describing the boundary of a region in projection planes (axial, sagittal or coronal) could be used to reconstruct the surface-representation of the 3D outer shell of the region. The latter could then be resliced in directions complementary to the drawing-direction and these complementary contours could be loaded in all tree cardinal views. In addition the surface object could be displayed using the SurfaceViewer. A pre-loading data crop and sub-sampling module allows the user to load and view practically data of any size. This is especially important when viewing cryotome, histological or stained data-sets which may reach 1GB (109 bytes) in size. The user could overlay several pre-registered volumes, change intensity colors and ranges and the inter-volume opacities to visually inspect similarities and differences between the different subjects/modalities. Several image-processing aids provide histogram plotting, image-smoothing, etc. Specific Features: * Region description DataBase * Moleculo-genetic database * Brain anatomical data viewer * BrainMapper tool * Surface (LightWave objects/scenes) and Volume rendering tools * Interactive Contour Drawing tool Implementation Issues: * Applet vs. Application - the software is available as both an applet and a standalone application. The former could be used to browse data from within the LONI database, however, it imposes restrictions on file-size, Internet connection and network-bandwidth and client/server file access. The later requires a local install and configuration of the LONI_Viz software * Extendable object-oriented code (Java), computer architecture independent * Complete online software documentation is available at http://www.loni.ucla.edu/LONI_Viz and a Java-Class documentation is available at http://www.loni.ucla.edu/~dinov/LONI_Vis.dir/doc/LONI_Viz_Java_Docs.htmlbrain, atlas, visualization, gene mapping, atlas application, magnetic resonance, surface analysisSCR_000765(LONI Visualization Tool, RRID:SCR_000765)Laboratory of Neuro Imaging AgingNCRR, NIA, NIMH, NLM, NSFlisted by: NeuroImaging Tools and Resources Collaboratory (NITRC), BiositemapsPMID:16598642Last checked downnif-0000-23313http://www.nitrc.org/projects/incf_loni-vizhttp://www.loni.ucla.edu/Software/LOVE
Knowledge Engineering from Experimental DesignResource, software resource, software applicationKnowledge engineering software for reasoning with scientific observations and interpretations. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a "neural connection matrix" interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. The KEfED model is designed to provide a lightweight representation for scientific knowledge that is (a) generalizable, (b) a suitable target for text-mining approaches, (c) relatively semantically simple, and (d) is based on the way that scientist plan experiments and should therefore be intuitively understandable to non-computational bench scientists. The basic idea of the KEfED model is that scientific observations tend to have a common design: there is a significant difference between measurements of some dependent variable under conditions specified by two (or more) values of some independent variable.experimental design, observation, interpretation, reasoning, experimental data, observational assertion, knowledge engineering, javaSCR_001238(Knowledge Engineering from Experimental Design, RRID:SCR_001238)Biomedical Informatics Research Network NCRR, NIGMS, NIMHrelated to: Bioscholar, listed by: FORCE11PMID:21859449Last checked downnif-0000-07745
NRF ContactsResource, data set, people resource, data or information resourceThis resource provides a list of federal program officials in the neurosciences. An informal compendium of names and contact information for nearly 300 research grant and scientific review administrators in 21 organizational units.director, military, neurodegenerative disease, program officer, 2008, neuroscienceSCR_001473(NRF Contacts, RRID:SCR_001473)Society for Neuroscience NIH, NIMH, U.S. Department of Health and Human ServicesLast checked downnif-0000-09488http://www.sfn.org/nrfcontacts
NeuroPediaResource, data or information resource, databaseA neuropeptide encyclopedia of peptide sequences (including genomic and taxonomic information) and spectral libraries of identified MS/MS spectra of homolog neuropeptides from multiple species.proteomics, peptide, neuropeptide, mass spectrometry assay, peptide sequence, spectrum, homologSCR_001551(NeuroPedia, RRID:SCR_001551)Center for Computational Mass Spectrometry NCRR, NHLBI, NIDA, NIMH, NINDSPMID:21821666Last checked downnlx_152894
Research Services Branch National Institutes of Mental HealthResource, portal, data or information resourcePortal for NIH, NIMH, and NINDS scientific and computer resources including Mac sites, PC sites, Linux sites, intramural programs, intranet and the NIH JumpStart and Directory.mac, pc, linuxSCR_001633(Research Services Branch National Institutes of Mental Health, RRID:SCR_001633)National Institutes of Health NIMH, NINDSLast checked downnlx_156832
MPIDBResource, data or information resource, databaseDatabase that collects and provides all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 26,578 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 68,346 additional evidences based on interaction conservation, co-purification, and 3D domain contacts (iPfam, 3did). (spoke/matrix) binary interactions inferred from pull-down experiments are not included.3d domain, conservation, co-purification, interaction, microbial, protein, microbial interaction, protein interaction, interaction conservation, interaction co-purification, 3d domain contact, protein-protein interaction, microbial protein, microbiologySCR_001898(MPIDB, RRID:SCR_001898)J. Craig Venter Institute Indgen Life Technologies, J. Craig Venter Institute, NIH, NIMHrelated to: IMEx - The International Molecular Exchange Consortium, IntAct, Database of Interacting Proteins, BIND, MINT, Interaction Reference Index, IMEx - The International Molecular Exchange Consortium, PSICQUIC Registry, listed by: re3data.orgPMID:18556668Last checked downnif-0000-10467http://jcvi.org/mpidb/
International Consortium for Brain MappingResource, database, reference atlas, software resource, service resource, storage service resource, atlas, data repository, data or information resourceA probabilistic reference system for the human brain, including tools to establish this reference system for structural and functional anatomy on both macroscopic (in vivo) and microscopic (post mortem) levels. The project has expanded the neuroinformatics tools for data sharing and created a Conforming Site System that allows laboratories worldwide to contribute data to the evolving atlas. Through the implementation of the ICBM data sharing policy space, they are fostering data exchange while still providing for scientific credit assignment and subject confidentiality. The ICBM atlas collection consists of the ICBM Template, a tool developed to provide a reference that includes both a set of coordinates and the associated anatomical labels; the ICBM 452 T1 atlas, an average of T1-weighted MRIs of normal young adult brains, the ICBM probabilistic atlases, and the newly released Cytoarchitectonic Atlas. The ICBM Subject Database is a web-based database infrastructure that simplifies image dataset collection, organization and dissemination. A web interface provides the means to query the data base using a combination of subject demographics and scan-related attributes. Authorized users may view representations of the data and form collections of datasets that can be downloaded or fed directly into the Pipeline environment for distributed processing and analysis. The current releases of ICBM related software are available for use by researchers. Links are provided to the various download sites. New releases are continually being tested and evaluated.fmri, genetics, anatomy, architecture, atlas, brainstem, cerebellum, cortex, gray matter, histology, imaging, map, morphology, mri, neuroinformatics, pet, receptor, segmentation, subcortical, volume, warping, white matter, brain, early adult human, structural anatomy, functional anatomy, in vivo, post mortem, neuroanatomy, image collectionSCR_001948(International Consortium for Brain Mapping, RRID:SCR_001948)Laboratory of Neuro Imaging NormalNIMHrelated to: MINC/AtlasesLast checked downnif-0000-00103http://www.loni.ucla.edu/ICBM/
OSAResource, software resource, software applicationSoftware application that allows the researcher to evaluate evidence for linkage even when heterogeneity is present in a data set. This is not an unusual occurrence when studying diseases of complex origin. Families are ranked by covariate values in order to test evidence for linkage among homogeneous subsets of families. Because families are ranked, a priori covariate cutpoints are not necessary. Covariates may include linkage evidence at other genes, environmental exposures, or biological trait values such as cholesterol, age at onset, and so on.gene, genetic, genomic, c++, unix, solaris, linuxSCR_002016(OSA, RRID:SCR_002016)Duke University; North Carolina; USA NIMHlisted by: Genetic Analysis SoftwareReferences (2)Last checked downnlx_154504http://wwwchg.duhs.duke.edu/software/osa.html
VoxBoResource, software resource, image analysis software, image processing software, data processing software, software applicationSoftware package for brain image manipulation and analysis, focusing on fMRI and lesion analysis. VoxBo can be used independently or in conjunction with other packages. It provides GLM-based statistical tools, an architecture for interoperability with other tools (they encourage users to incorporate SPM and FSL into their processing pipelines), an automation system, a system for parallel distributed computing, numerous stand-alone tools, decent wiki-based documentation, and lots more.fmri, neuroimaging, brain, functional, statistical, volume, preprocessing, analysis, display, format conversion, linear, three dimensional display, workflow, lesion, analyze, c++, console (text based), dicom, image display, linux, macos, microsoft, magnetic resonance, nifti, no input/output (daemon), overlap metrics, posix/unix-like, quantification, regression, resampling, sinc function interpolation, spatial transformation, statistical operation, visualization, windowsSCR_002166(VoxBo, RRID:SCR_002166)neurodebian NIDA, NIH, NIMHlisted by: NeuroImaging Tools and Resources Collaboratory (NITRC), BiositemapsPMID:22348882Last checked downnif-0000-00353http://www.voxbo.org/
Mindboggle-101 atlasesResource, atlas, data or information resourceComplete set of free, publicly accessible, downloadable atlases, templates, and individual manually labeled brain image data, the largest collection of publicly available, manually labeled human brains in the world!\\n\\nhttp://journal.frontiersin.org/article/10.3389/fnins.2012.00171/fullclinical neuroinformatics, computational neuroscience, mgh/mgz, magnetic resonance, nifti, image collectionSCR_002439(Mindboggle-101 atlases, RRID:SCR_002439)NIMHlisted by: NeuroImaging Tools and Resources Collaboratory (NITRC)PMID:23227001Last checked downnlx_155814http://www.nitrc.org/projects/mindboggle101
Spatial Analysis 3DResource, software resource, software applicationA user-friendly, graphical user interface (GUI) that allows statistical and visual manipulations of real and simulated three-dimensional spatial point patterns. The analyses use files containing sets of X, Y, Z coordinates. These point patterns are frequently coordinates of cells of specific cell classes within in volumes of tissue derived from microscopy analyses. The analyses are scale independent so spatial analyses of coordinates from larger and smaller scale distributions are possible. The software can also generate sample sets of X, Y, Z coordinates for program exploration and modeling purposes.eeg, meg, electrocorticography, matlab, modeling, magnetic resonance, position, quantification, simulation, statistical operation, cell, microscopySCR_002563(Spatial Analysis 3D, RRID:SCR_002563)University of California at Santa Barbara; California; USA NEI, NIMHlisted by: NeuroImaging Tools and Resources Collaboratory (NITRC)PMID:18644136Last checked downnlx_155969http://www.nitrc.org/projects/sa3d
SumsDBResource, data analysis service, database, analysis service resource, production service resource, service resource, storage service resource, atlas, image repository, data repository, data or information resourceTHIS 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 figuressegmentation, 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, neuroanatomySCR_002759(SumsDB, RRID:SCR_002759)Washington University School of Medicine in St. Louis; Missouri; USA Mental disease, Neurological disorder, NormalHuman Brain Project, NASA, National Partnership for Advanced Computational Infrastructure, NCI, NIMH, NLM, NSFrelated to: Computerized Anatomical Reconstruction and Editing Toolkit, Integrated Manually Extracted Annotation, used by: NIF Data Federation, listed by: Biositemaps, NeuroImaging Tools and Resources Collaboratory (NITRC), re3data.orgLast checked downnif-0000-00016http://brainvis.wustl.edu/wiki/index.php/Sums:About http://www.nitrc.org/projects/sumsdb
NIH ImageResource, source code, data processing software, image analysis software, software application, software resource, image processing softwarePublic image processing and analysis program for Macintosh.image processing application, public image processing software, imagejSCR_003073(NIH Image, RRID:SCR_003073)National Institutes of Health , National Institute of Mental Health NIMH, NINDSrelated to: ImageJ, BrainImage Software, Object-ImageLast checked downnif-0000-30469
Neuroimaging Informatics Technology InitiativeResource, knowledge environment, training resourceCoordinated and targeted service, training, and research to speed the development and enhance the utility of informatics tools related to neuroimaging. The initial focus will be on tools that are used in fMRI. If NIfTI proves useful in addressing informatics issues in the fMRI research community, it may be expanded to address similar issues in other areas of neuroimaging. Objectives of NIfTI * Enhancement of existing informatics tools used widely in neuroimaging research * Dissemination of neuroimaging informatics tools and information about them * Community-based approaches to solving common problems, such as lack of interoperability of tools and data * Unique training activities and research career development opportunities to those in the tool-user and tool-developer communities * Research and development of the next generation of neuroimaging informatics toolsneuroimaging, neuroinformatics, technology, service, training, research, mri, fmri, software, algorithm or reusable library, c, computed tomography, developers, information resource, java, matlab, magnetic resonance, nifti, other information resource, pet, spect, softwareSCR_003141(Neuroimaging Informatics Technology Initiative, RRID:SCR_003141)National Institute of Mental Health NIH Blueprint for Neuroscience Research, NIMH, NINDSrelated to: GIFTI, used by: Stark Cross-Sectional Aging, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)Last checked downnif-0000-00561http://www.nitrc.org/projects/niftihttp://www.bic.mni.mcgill.ca/nifti/
Datasharing.netResource, topical portal, portal, data or information resourceThe U.S. National Institutes of Health Final NIH Statement on Sharing Research Data (NIH-OD-03-032) is now in effect. It specifies that all high-direct-cost NIH grant applications include plans for sharing of research data. To support and encourage collegial, enabling, and rewarding data sharing for neuroscience and beyond, the Laboratory of Neuroinformatics at Weill Medical College of Cornell University has established this site. A source of, and portal to, tools and proposals supporting the informed exchange of neuroscience data.data management, neuroinformatics, data sharingSCR_003312(Datasharing.net, RRID:SCR_003312)Weill Cornell Medical College; New York; USA Human Brain Project, NIMH, NINDS, NSFLast checked downnif-0000-00061
LONI SoftwareResource, software resource, software application, software repository, data analysis software, data processing softwareA portal of software resources offered by UCLA's Laboratory of Neuro Imaging. LONI Webapps allow users to analyze, visualize and interact with neuroscience data directly from their web browser. LONI aims to encourage communication between users and LONI software engineers in order to improve the effectiveness of our software and to promote its use by researchers worldwide. We have expanded our software website to include more tools, training and support. Be sure to visit LONI Forums and discuss our tools with other end-users as well as our dedicated LONI staff.visualization, shape analysis, registration, statistical analysis, data management, image processing, pre=processing, segmentation, surface modeling, modelSCR_003323(LONI Software, RRID:SCR_003323)University of California at Los Angeles; California; USA DOE, NCRR, NIBIB, NIGMS, NIH, NIMH, NINDSrelated to: Mouse Atlas Project, listed by: 3DVC, BiositemapsLast checked downnif-0000-00063http://www.loni.ucla.edu/Software/
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