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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)

Physical Resource or Software Tool Software

16,796 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
SciPipeResource, source code, workflow software, data processing software, software library, software application, software resource, software toolkitSoftware tool for writing scientific workflows of shell commands that depend on each other in Go programming language. Workflow library for agile development of complex and dynamic bioinformatics pipelines. Used in bioinformatics and cheminformatics, but works for any problem involving pipelines of commandline applications.writing, scientific, workflow, shell, command, line, application, processing, software, GoSCR_017086(SciPipe, RRID:SCR_017086)European Union’s Horizon 2020 research and innovation programme, National Bioinformatics Infrastructure Sweden (NBIS), Swedish e-Science Research Centre (SeRC), Swedish strategic research programme eSSENCErelated to: golangDOI:10.1101/380808Last checked up10.5281/zenodo.1157941,
FSLResource, software resource, software toolkit, software librarySoftware library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas.dti, brain, imaging, data, structural, mri, diffusion, function, preprocessing, analysis, statistical, tractography, atlas, neuroimaging, parameter, reconstruction, volumetric, segmentation, independent, component, temporal, transformationSCR_002823(FSL, RRID:SCR_002823)University of Oxford; Oxford; United Kingdom BBSRC, EPSRC, GlaxoSmithKline, MRC, Pfizerrelated to: Rodent Brain Extraction Tool, WU-Minn Consortium: Human Connectome Project, BASH4RfMRI, DW-MRI registration in FSL, FSL extensions, Diffusion MRI of Traumatic Brain Injury, Segmentation of Hippocampus Subfields, masked ICA (mICA) Toolbox, used by: Spinal Cord Toolbox, Functional Real-time Interactive Endogenous Neuromodulation and Decoding (FRIEND), XFSL: An FSL toolbox, CMIND PY, Automatic Analysis, uses: Neuroimaging Data Model, listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)References (3)Last checked upbirnlex_2067, SCR_007368, nif-0000-00305,
United States Department of Health and Human Services granting agencyResource, government granting agency States Department of Health and Human Services granting agency, RRID:SCR_011596)Last checked downbirnlex_2432
U.S. Department of AgricultureResource, government granting agencyA United States Federal Executive Department to develop and execute policy on farming, agriculture, and food. It aims to meet the needs of farmers and ranchers, promote agricultural trade and production, work to assure food safety, protect natural resources, foster rural communities and end hunger, in America and abroad. USDA also participates in overseas aid programs, by providing surplus foods to developing countries to support development programs with other organizations. ( Department of Agriculture, RRID:SCR_011486)Last checked upC0085410
Health Care OrganizationResource, institutionAn organization that provides healthcare services or that is involved in the provision of health care activities. Groupings or subdivisions of an organization, such as departments, may also be considered as organizations where there is a need to identify them.SCR_011275(Health Care Organization, RRID:SCR_011275)Last checked upC43960
SimThyrResource, software resource, software application, simulation softwareSimulation software for thyroid homeostasis, which is based on a published nonlinear model of pituitary-thyroid feedback control. Specifically, the program simulates pituitary thyroid feedback control, which allows users to study the relationship between structure and behaviour of thyroid homeostasis.thyroid, homeostasis, simulation, software, modelling, pituitary, modelSCR_014351(SimThyr, RRID:SCR_014351)Ludwig-Maximilians-University; Bavaria; Germany , Ruhr University Bochum; North Rhine-Westphalia; Germany hypothyroidism, hyperthyroidism, thyrotoxicosis, resistance to thyroid hormone (RTH Beta), non-thyroidal illness syndrome (NTIS), euthyroid sick syndrome (ESS), thyroid allostasis in critical illness, tumors, uremia and starvation (TACITUS), subclinical thyroid diseases, syndrome TDOI:10.1080/01969720490443354, DOI:10.1155/2012/351864, DOI:10.5281/zenodo.1303822, PMID:23365787Last checked downDOI:10.5281/zenodo.1303822
Brookhaven National Laboratories; New York; USAResource, national laboratoryOne of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. Brookhaven is operated and managed for DOE''s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization. Id=nlx_56211SCR_011123(Brookhaven National Laboratories; New York; USA, RRID:SCR_011123)United States Department of Energy Last checked upGAZ:00159027
Brain Imaging Data StructureResource, narrative resource, standard specification, data or information resourceStandard specification for organizing and describing outputs of neuroimaging experiments.neuroimaging, research, organization, output, data sharing, consensusSCR_016124(Brain Imaging Data Structure, RRID:SCR_016124)used by: OpenNeuro, SPARC Project, listed by: BioSharing, submitted by: Resource Identification PortalPMID:27326542Last checked down
Automatic Tractography-based Parcellation PipelineResource, software resource, software application, workflow software, data processing softwareIntegrated pipeline for tractography-based brain parcellation with automatic processing and massive parallel computing. ATPP offers a CLI version for parcellating multiple brain regions and a GUI version for parcellating a specific brain region.\\n\\n" ATPP completely follows the scientific cultural shift to open science, which aims at making scientific research including journal papers, lab notes, data, and, of course, workflow tools, accessible and transparent to all levels of society. ATPP is publicly accessible in Neuroimaging Informatics Tools and Resources Clearinghouse8 (NITRC) ( Its source codes are hosted in GitHub9 (;, under the GNU generic purpose license version 310 (GPLv3), and are welcome to download and fork. The Digital Object Identifiers (DOIs) providing a persistent way to make digital data easily and uniquely citable was created from Zenodo11 platform with those GitHub repositories (ATPP CLI v2.0.0, doi:; ATPP GUI v2.0.0, doi: "pipeline, integrated pipeline, tractography, brain, parcel, gui, workflowSCR_014815(Automatic Tractography-based Parcellation Pipeline, RRID:SCR_014815)Chinese Academy of Sciences; Beijing; China National Natural Science Foundation of China10.13039/501100001809 911323013162010390581501179listed by: NeuroImaging Tools and Resources Collaboratory (NITRC), submitted by: Resource Identification PortalLast checked up,,
NIXResource, interchange format, data processing software, software application, standard specification, narrative resource, data storage software, software resource, neuroinformatics tool, data or information resourceSoftware that defines a data model for annotated scientific datasets. It includes data together with metadata, and a corresponding file format based on HDF5 for storing and sharing such, model, metadata, scientific, integration, file, format, annotation, hdf5, datasetSCR_016196(NIX, RRID:SCR_016196)German Neuroinformatics Node , Ludwig-Maximilians-University; Bavaria; Germany BMBFused by: EEGbase, uses: Open metadata mark up languageDOI:10.3389/conf.fninf.2014.18.00027Last checked up
BioPortainerResource, software resource, software application, data analysis software, data processing softwareOpen source software designed in modular way, aimed at facilitating user interaction with Docker environments in three different computational layers like infrastructure, platform and application.docker, bioportainer, user, interaction, docker, environment, infrastructure, platform, applicationSCR_017058(BioPortainer, RRID:SCR_017058)Last checked up
eXpression2KinasesResource, software resource, software applicationSoftware tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures.inferred, network, transcription, factor, protein, kinase, regulate, expression, gene, analysis, combineSCR_016307(eXpression2Kinases, RRID:SCR_016307)NCRR, NIDDK, NIGMS, NLMPMID:22080467Last checked up
Tip-Tilt-Z Sample PositionerResource, material resourcePositioner for automated rotation of a head-fixed rodent specimen about the anterior-posterior and medio-lateral axes for imaging or other purposes. Provides automated Z translation and can be customized to accommodate various head bar designs.instrument, positioner, automated, rotation, head, fixed, rodent, imagingSCR_016528(Tip-Tilt-Z Sample Positioner, RRID:SCR_016528)Janelia Research Last checked upJanelia 2016-027
Neurodatabase.orgResource, service resource, data or information resource, data repository, storage service resource, databaseTHIS RESOURCE IS NO LONGER IN SERVICE, documented on June 09, 2015. A repository of neurophysiology data conforming to BrainML data models and protocols: BrainML-formatted experimental data submissions are published in searchable, browsable form. Registered users may submit new experiments. The site contains spike trains, voltage time series, and some derived histograms from single cell and multi-unit activity. The database focuses on in vivo somatosensory and visual activity during task performance. This resource contains only a few datasets, but they are of high quality and have been used for reanalysis by several parties. There are three primary interfaces for querying data from this repository: a web-based browse interface, a web-based HTML query form, and a Java web start desktop application. In addition, there is an XML interface useful for direct access by software clients. To download the source code, please read and acknowledge the license agreement.neurophysiology, source code, spike train, voltage time series, histogram, single cell, multi-unit, in vivo, somatosensory, visual, task, data setSCR_007091(, RRID:SCR_007091)Weill Cornell Medical College; New York; USA used by: NIF Data Federation, uses: BrainMLLast checked downnif-0000-00001
L-MeasureResource, image analysis software, data processing software, software application, service resource, software resource, image processing softwareA freely available software tool available for the Windows and Linux platform, as well as the Online version Applet, for the analysis, comparison and search of digital reconstructions of neuronal morphologies. For the quantitative characterization of neuronal morphology, LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions, including: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available for either online use on any Java-enabled browser and platform or may be downloaded for local execution under Windows and Linux.neuronal morphology, neuroinformatics, branching analysis, digital reconstruction, analysis, comparisonSCR_003487(L-Measure, RRID:SCR_003487)Computational Neuroanatomy Group Human Brain Project, NINDSlisted by: 3DVC, NeuroImaging Tools and Resources Collaboratory (NITRC)PMID:18451794Last checked upnif-0000-00003
ModelDBResource, software resource, software repository, data or information resource, databaseCurated database of published models so that they can be openly accessed, downloaded, and tested to support computational neuroscience. 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 the simulation results from which authors derived their published insights and conclusions.repository, collection, network, neuron, computational, neuroscience, model, simulation, neural, dataSCR_007271(ModelDB, RRID:SCR_007271)Yale University; Connecticut; USA Human Brain Project, NCI, NIDCD, NIMH, NINDSrelated to: SimToolDB, NeuronDB, NeuronVisio, Integrated Manually Extracted Annotation, used by: NIF Data Federation, listed by: 3DVC, Biositemaps, Integrated Models, lists: ModelRun, works_with: MicrocircuitDBReferences (3)Last checked upnif-0000-00004
NeuroMorpho.OrgResource, service resource, data or information resource, data repository, storage service resource, databaseCentrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications that contains some of the most complete axonal arborizations digitally available in the community. Each neuron is represented by a unique identifier, general information (metadata), the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. It contains contributions from over 100 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. Users may browse by species, brain region, cell type or lab name. Users can also download morphological reconstructions for research and analysis. Deposition and distribution of reconstruction files ultimately prevents data loss. Centralized curation and annotation aims at minimizing the effort required by data owners while ensuring a unified format. It also provides a one-stop entry point for all available reconstructions, thus maximizing data visibility and impact.neuron, morphological reconstruction, morphometry, axonal arborization, digital neuronal reconstruction, neuronal reconstruction, neuronal morphology, data sharing, annotation, brain region, neocortex, digital reconstruction, neurogenetics, neurochemistry, neuroscience, neurologySCR_002145(NeuroMorpho.Org, RRID:SCR_002145)George Mason University; Virginia; USA MURI, NINDSrelated to: DONE: Detection of Outlier NEurons, NIF Literature, Computational Neurobiology and Imaging Center, Integrated Manually Extracted Annotation, used by: NIF Data Federation, listed by:, NeuroImaging Tools and Resources Collaboratory (NITRC)References (3)Last checked downnif-0000-00006
Cell Centered DatabaseResource, database, service resource, storage service resource, image repository, data repository, data or information resourceTHIS RESOURCE IS NO LONGER IN SERVICE, documented June 5, 2017. It has been merged with Cell Image Library. Database for sharing and mining cellular and subcellular high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging that makes unique and valuable datasets available to the scientific community for visualization, reuse and reanalysis. Techniques range from wide field mosaics taken with multiphoton microscopy to 3D reconstructions of cellular ultrastructure using electron tomography. Contributions from the community are welcome. The CCDB was designed around the process of reconstruction from 2D micrographs, capturing key steps in the process from experiment to analysis. The CCDB refers to the set of images taken from microscope the as the Microscopy Product. The microscopy product refers to a set of related 2D images taken by light (epifluorescence, transmitted light, confocal or multiphoton) or electron microscopy (conventional or high voltage transmission electron microscopy). These image sets may comprise a tilt series, optical section series, through focus series, serial sections, mosaics, time series or a set of survey sections taken in a single microscopy session that are not related in any systematic way. A given set of data may be more than one product, for example, it is possible for a set of images to be both a mosaic and a tilt series. The Microscopy Product ID serves as the accession number for the CCDB. All microscopy products must belong to a project and be stored along with key specimen preparation details. Each project receives a unique Project ID that groups together related microscopy products. Many of the datasets come from published literature, but publication is not a prerequisite for inclusion in the CCDB. Any datasets that are of high quality and interest to the scientific community can be included in the CCDB.electron microscope, light microscopy, electron tomography, electron microscopy, image, cell, microscopy, tomographySCR_002168(Cell Centered Database, RRID:SCR_002168)University of California at San Diego; California; USA related to: Cell Image Library (CIL), Cell Image Library (CIL), Whole Brain Catalog, Integrated Manually Extracted Annotation, used by: NIF Data Federation, Integrated Datasets, listed by: re3data.orgReferences (2)Last checked upnif-0000-00007
Cerebellar Development Transcriptome DatabaseResource, atlas, database, data or information resourceTranscriptomic information (spatiotemporal gene expression profile data) on the postnatal cerebellar development of mice (C57B/6J & ICR). It is a tool for mining cerebellar genes and gene expression, and provides a portal to relevant bioinformatics links. The mouse cerebellar circuit develops through a series of cellular and morphological events, including neuronal proliferation and migration, axonogenesis, dendritogenesis, and synaptogenesis, all within three weeks after birth, and each event is controlled by a specific gene group whose expression profile must be encoded in the genome. To elucidate the genetic basis of cerebellar circuit development, CDT-DB analyzes spatiotemporal gene expression by using in situ hybridization (ISH) for cellular resolution and by using fluorescence differential display and microarrays (GeneChip) for developmental time series resolution. The CDT-DB not only provides a cross-search function for large amounts of experimental data (ISH brain images, GeneChip graph, RT-PCR gel images), but also includes a portal function by which all registered genes have been provided with hyperlinks to websites of many relevant bioinformatics regarding gene ontology, genome, proteins, pathways, cell functions, and publications. Thus, the CDT-DB is a useful tool for mining potentially important genes based on characteristic expression profiles in particular cell types or during a particular time window in developing mouse brains.gene expression, fluorescence, function, gene, gene chip, genome, bioinformatics, brain, cell, cerebellum, development, in situ hybridization, fluroescence differential display, cerebellar development, microarray, mining, mouse, mrna, ontology, pathway, protein, rt-pcr, molecular neuroanatomy resource, transcriptiome, spatiotemporal, cdna microarray, genechip, postnatal, histochemistry, image, postnatal developmentSCR_013096(Cerebellar Development Transcriptome Database, RRID:SCR_013096)RIKEN Brain Science Institute Brain development, Brain disorderINCF Japan Node, Japanese Ministry of Education Culture Sports Science and Technology MEXT, Japan Science and Technology Agency, Japan Society for the Promotion of Sciencerelated to: Gene Ontology, RIKEN integrated database of mammalsPMID:18603407Last checked upnif-0000-00008
GenePaint.orgResource, atlas, expression atlas, data or information resource, reference atlas, databaseA digital atlas of gene expression patterns in the developing and adult mouse. Several reference atlases are also available through this site. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. Sections were labeled using non radioactive in situ hybridization with riboprobes and annotated for level of gene expression (not detected, weak, medium, strong) and pattern (ubiquitous, regional, scattered). Sections are available from several developmental ages: E10.5, E14.5 (whole embryos), E15.5, P7 and P56 (brains only). To retrieve expression patterns, search by gene name, site of expression, GenBank accession number or sequence homology. For viewing expression patterns, features a virtual microscope tool that enables zooming into images down to cellular resolution.gene expression, adult mouse, annotated, c57bl6, mouse, mouse embryo, mrna, non radioactive in situ hybridization, light microscopy, molecular neuroanatomy resource, in situ hybridization, embryonic, postnatal, adult, brain, head, annotation, rna probe, sequence, anatomical structureSCR_003015(, RRID:SCR_003015)Max Planck Institute for Biophysical Chemistry; Gottingen; Germany BMBF, Burroughs Wellcome Fund, European Union, Max Planck Society, Merck Genome Research Institute, NINDS, Romansky EndowmentReferences (2)Last checked upnif-0000-00009
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