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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: Aug 10, 2019)

Physical Resource or Software Tool Software

452 Results - per page

Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
DicomWorksResource, software resource, software applicationSoftware to help users work with DICOM files by organizing, managing and analyzing them. Key features: * a smart DICOM viewer with 4 panel display, annotations, arrows, multimodality synchronization, etc... * an export wizard to the most common picture or movie file formats * an export wizard to Microsoft PowerPoint * the most simple and compatible DICOM CD-ROM reader * the most simple and smart DICOM CD-ROM WRITER * an archiving solution with lossless compression of the data * a DICOM creation module to dicomize images from any image source (even video capture) * e-mail or FTP import end export functions (teleradiology) * 16 native localized versionsdicom, windows, radiology, image analysis, anonymization, protocol, export, powerpoint, surface analysis, visualizationSCR_001195(DicomWorks, RRID:SCR_001195)listed by: BiositemapsLast checked upnif-0000-00288
flowCyBarResource, software resourceA software package to analyze flow cytometric data using gate information to follow population / community package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, clustering, visualizationSCR_002319(flowCyBar, RRID:SCR_002319)Bioconductor listed by: OMICtoolsLast checked upOMICS_05597
vmtk in 3DSlicerResource, segmentation software, image analysis software, data processing software, software application, software resource, software toolkitA series of modules which enable functions of the Vascular Modeling Toolkit ( in 3D Slicer ( The functionality includes vessel enhancement filtering, level set segmentation, centerline computation, network extraction and branch splitting.dicom, macos, microsoft, modeling, magnetic resonance, nrrd, posix/unix-like, python, segmentation, visualization, win32 (ms windows), windowsSCR_002579(vmtk in 3DSlicer, RRID:SCR_002579)Vascular Modeling Toolkit related to: 3D Slicer, Insight Segmentation and Registration Toolkit, listed by: NITRCLast checked downnlx_155981
GPVizResource, software resourceA versatile Java-based software used for dynamic gene-centered visualization of genomic regions and/or variants.gene, visualization, genomic, variant, bioinformatics, javaSCR_000346(GPViz, RRID:SCR_000346)listed by: OMICtoolsLast checked upOMICS_00915
DTI and Fibertools Software PackageResource, software resource, software application, image processing software, data processing software, software toolkitImplemented under MATLAB, this DTI image processing toolbox provides import-filters for several MR file standards, a processing unit to calculate the diffusion tensors; several GUI based tools to calculate fiber tracks and to evaluate the DTI dataset. The results can be filed as images with 3D impression or can be logged in formatted ASCII files. Tools and features: * DTI Processing Unit: Calculates the diffusion tensors and their eigenvalues and eigenvectors. Different file formats are supported (like DICOM, Bruker, binary files, Matlab structures). The standard SIEMENS and GE diffusion encoding schemes are supported; other schemes have to be defined in a separate text, .m or .mat file. * FiberTracking: ** Fiber tracking is realized by using the FACT algorithm (Mori et al., Annal. Neurol 1999). ** Probabilistic tracking realized by using the PiCo (Parker et al., JMRI 2003) approach but with DTI data as basis. It is possible to extract pathways between two seeds by combining two maps (Kreher et al., NeuroImage 2008). ** Global Fiber Tracking on basis of HARDI or DTI data. The method is based on the approach reported in (Marco Reisert et al: Global fiber reconstruction becomes practical. NeuroImage 54(2):955-62) * FiberViewer: ** Visualization and Navigation through different data modalities like DTI maps, fiber tracks, diffusion main directions. ** Supports different kinds of DTI maps (e.g. FA, Trace, lambda images ) ** Creation and manipulation of mask based ROIs. ** Selection of streamline fibers ** Visualization of probabilistic fiber tracking results ** Documentation by logging statistics of ROIs and fiber tracks into text files. ** Import/Export from/to ANALYZE or Nifti * 3D Visualizer: Visualization of map slices, ROIs, and fiber tracks with 3D impression. * Batch Editor: Automatic processing of high amounts of data. Possibility to link processing with SPM8 easily.diffusion, dti, fiber tracking, diffusion tensor, visualization, navigationSCR_001641(DTI and Fibertools Software Package, RRID:SCR_001641)University of Freiburg; Baden-Wurttemberg; Germany related to: Diffusion MRI of Traumatic Brain InjuryLast checked upnlx_153913
DegustResource, software resource, analysis service resource, data analysis service, service resource, production service resourceAn interactive web tool for visualizing differential gene expression data.differential gene expression, differential expression, gene expression, visualizationSCR_001878(Degust, RRID:SCR_001878)Monash University; Melbourne; Australia listed by: OMICtoolsLast checked upOMICS_01934
SeqMonkResource, software resourceSoftware tool to visualize and analyse high throughput mapped sequence, high throughput sequencing, mapped, visualization, analysisSCR_001913(SeqMonk, RRID:SCR_001913)Babraham Institute listed by: OMICtoolsLast checked upOMICS_01936
SCANCO Medical microCT 100 systemResource, material resourceMicro Computed Tomography 100 scanner for 3D imaging of specimens in vitro supplied with software for scanning, 3D analysis, visualization, image management and data import and export by SCANCO Medical AG.SCANCO, micro, CT, computed, tomography, scanner, 3D, imaging, speciment, in vitro, analysis, visualization, image, dataSCR_017119(SCANCO Medical microCT 100 system, RRID:SCR_017119)Last checked up
OGDrawResource, data processing software, software application, data visualization software, service resource, software resource, software toolkitSoftware package for graphical visualization of organellar genomes. Converts annotations in GenBank format into graphical maps. Used to create visual representations of circular and linear annotated genome sequences provided as GenBank files or accession numbers.graphical, visualization, organellar, genome, convert, annotation, GenBank, format, map, DNA, sequenceSCR_017337(OGDraw, RRID:SCR_017337)Max Planck Societyworks_with: GenBankPMID:30949694Last checked up
EpsonResource, material resource, instrument supplierA commercial vendor of visualization software, factory automation equipment and electric components.visualization, software, factory, automation, equipment, electric, components, printer, touchscreenSCR_000787(Epson, RRID:SCR_000787)Last checked upnif-0000-30524
Computational Morphometry ToolkitResource, software resource, software toolkit, software applicationA software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O. The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction; EPI unwarping), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear model). CMTK is implemented in C++ with parallel processing using POSIX Threads (SMP), OpenMP (SMP), Grand Central Dispatch (SMP), and CUDA (GPU). Supported file formats include Analyze (r/w), NIFTI (r/w), Nrrd (r/w), DICOM (read), BioRad (read). Data exchange with other toolkits, such as ITK, FSL, AFNI, SPM, etc. is thus easily accomplished.reusable library, analyze, anatomic, artifact removal, atlas application, c, c++, console (text based), cygwin, dicom, domain independent, format conversion, image display, image reconstruction, image-to-image, labeling, linear, linux, macos, microsoft, magnetic resonance, nifti-1, nrrd, posix/unix-like, principal component analysis, region of interest, registration, regression, resampling, segmentation, sh/bash, spatial transformation, statistical operation, sunos/solaris, two dimensional display, unix shell, visualization, warping, win32 (ms windows), windows, workflowSCR_002234(Computational Morphometry Toolkit, RRID:SCR_002234)neurodebian listed by: NITRCLast checked upnlx_155536
FunSimMatResource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resourceFunSimMat is a comprehensive resource of semantic and functional similarity values. It allows ranking disease candidate proteins for OMIM diseases and searching for functional similarity values for proteins (extracted from UniProt), and protein families (Pfam, SMART). FunSimMat provides several different semantic and functional similarity measures for each protein pair using the Gene Ontology annotation from UniProtKB and the Gene Ontology Annotation project at EBI (GOA). There are several search options available: Disease candidate prioritization: * Rank candidate proteins using any OMIM disease entry * Compare a list of proteins to any OMIM disease entry * Compare all human proteins to any OMIM disease entry Functional similarity: * Compare one protein / protein family to a list of proteins / protein families * Compare a list of GO terms to a list of proteins / protein families Semantic similarity: * For a list of GO terms, FunSimMat performs an all-against-all comparison and displays the semantic similarity values. FunSimMat provides an XML-RPC interface for performing automatic queries and processing of the results as well as a RestLike Interface. Platform: Online toolfunctional similarity value, protein family, protein similarity, semantic similarity value, similarity value, functional similarity, disease gene candidate prioritization, disease, protein, protein family, disease candidate prioritization, semantic similarity, gene ontology, visualization, annotation, database or data warehouseSCR_002729(FunSimMat, RRID:SCR_002729)Max-Planck-Institute for Informatics; Saarbrucken; Germany European Union, German National Genome Research Network, Klinische Forschergrupperelated to: Gene Ontology, listed by: Gene Ontology ToolsReferences (2)Last checked upnif-0000-02860
GoMapManResource, service resource, data or information resource, databaseAn open web-accessible resource for gene functional annotations in the plant sciences to facilitate improvement, consolidation and visualization of gene annotations across several plant species. It is based on the MapMan ontology, organized in the form of a hierarchical tree of biological concepts, which describe gene functions. Currently, genes of the model species Arabidopsis, potato, tomato, rice, and tobacco are included. The main features are (i) dynamic and interactive gene product annotation through various curation options; (ii) consolidation of gene annotations for different plant species through the integration of orthologue group information; (iii) traceability of gene ontology changes and annotations; (iv) integration of external knowledge about genes from different public resources; and (v) providing gathered information to high-throughput analysis tools via dynamically generated export files. All of the GoMapMan functionalities are openly available, with the restriction on the curation functions, which require prior registration to ensure traceability of the implemented changes.functional annotation, function, annotation, gene, visualization, ortholog, ontology, microarray, gene annotationSCR_005060(GoMapMan, RRID:SCR_005060)Jozef Stefan Institute; Ljubljana; Slovenia Slovenian Research Agencyrelated to: Gene Set Enrichment Analysis, MapMan, Biomine, SEGS, listed by: OMICtoolsPMID:24194592Last checked upOMICS_02280
PINGResource, software resourceSoftware program for probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.clustering, sequencing, statistics, visualization, chip-seq, short-readSCR_005394(PING, RRID:SCR_005394)Bioconductor listed by: OMICtoolsLast checked upOMICS_00513
Human Epigenome BrowserResource, source code, data analysis software, data processing software, software application, data set, software resource, data or information resourceSoftware tool for visualizing and interacting with whole-genome datasets. The browser currently hosts Human Epigenome Atlas data produced by the Roadmap Epigenomics project, but its use of advanced, multi-resolution data formats and its user-friendly interface make it possible for investigators to upload and visualize their own data as custom tracks. The Human Epigenome Browser is developed and maintained by the Epigenome Informatics Group at Washington University in St. Louis.epigenomics, genome browser, visualization, clustering, genome, sequencing, next-generation sequencing, virusSCR_006208(Human Epigenome Browser, RRID:SCR_006208) Roadmap Epigenomics Project , Washington University School of Medicine in St. Louis; Missouri; USA related to: VizHub, UCSC Genome Browser, Human Epigenome Atlas, listed by: OMICtoolsPMID:22127213Last checked upnlx_151754, OMICS_00629
SamscopeResource, software resourceA lightweight SAM/BAM file viewer that makes visually exploring next generation sequencing data intuitive and maybe even fun! Quickly and easily generate aggregate statistics from SAM/BAM files like coverage, polarity, and minor allele frequencies, then scroll and explore freely with a simple mouse based interface. Multiple windows can be synchronized for careful comparison across multiple experiments.c++, visualization, opengl, next generation sequencingSCR_006715(Samscope, RRID:SCR_006715)SourceForge listed by: OMICtoolsLast checked upOMICS_00892
IBASPM: Individual Brain Atlases using Statistical Parametric Mapping SoftwareResource, software resource, software toolkitThe aim of this work is to present a toolbox for structure segmentation of structural MRI images. All programs were developed in MATLAB based on a widely used fMRI, MRI software package, SPM99, SPM2, SPM5 (Wellcome Department of Cognitive Neurology, London, UK). Other previous works have developed a similar strategy for obtaining the segmentation of individual MRI image into different anatomical structures using a standardized Atlas. Have to be mentioned the one introduced by Montreal Neurological Institute (MNI) that merges the information coming from ANIMAL (algorithm that deforms one image (nonlinear registration) to match previously labelled) and INSECT (Cerebral Tissue Classification) programs for obtaining a suitable gross cortical structure segmentation (Collins et al, 1999). Here both, nonlinear registration and gray matter segmentation processes have been performed through SPM99, SPM2, SPM5 subroutines. Three principal elements for the labeling process are used: gray matter segmentation, normalization transform matrix (that maps voxels from individual space to standardized one) and MaxPro MNI Atlas. All three are combined to yield a good performance in segmenting gross cortical structures. The programs here can be used in general for any standardized Atlas and any MRI image modality. System Requirements: 1. The IBASPM graphical user interface (GUI) runs only under MATLAB 7.0 or higher. The non-graphical version runs under MATLAB 6.5 or higher. 2. Statistical Parametrical Mapping Software SPM2, SPM5 Main Functions: * Atlasing: Main function ( This file contains spm_select script from SPM5 toolbox and uigetdir script from MATLAB 7.0 ). * Auto_Labeling : Computes individual atlas. * Create_SPAMs : Constructs Statistical Probability Anatomy Maps (SPAMs). * Create_MaxProb : Creates Maximum Probability Atlas (MaxPro) using the SPAMs previously computed. * All_Brain_Vol : Computes whole brain volume masking the brain using the segmentation files (if the segmentation files does not exist it segments). * Struct_Vol : Computes the volume for different structures based on individual Atlas previously obtained by the atlasing process. * Vols_Stats : Computes mean and standard deviation for each structure in a group of individual atlases.segmentation, structural mri, image, label, brain, structure, volume, visualization, atlasing, anatomical structure, probability, statistics, mean, standard deviation, atlasSCR_007110(IBASPM: Individual Brain Atlases using Statistical Parametric Mapping Software, RRID:SCR_007110)Last checked upnlx_144301
Mayavi: 3D Scientific Data Visualization and Plotting Software ProjectResource, data visualization software, software application, data processing software, software resourceSoftware packages for 3D visualization: Mayavi2 for data visualization and TVTK for object manipulation.functionality, plot, scalar, scientific, vector, visualization, python, apiSCR_008335(Mayavi: 3D Scientific Data Visualization and Plotting Software Project, RRID:SCR_008335)Last checked upnif-0000-24918
NeuroptikonResource, data visualization software, software application, data processing software, software resourceNeuroptikon is a tool for visualizing and interacting with neural circuits. Sponsors: This resource is supported by Janelia Farms.circuit, interaction, neural, software, visualizationSCR_008369(Neuroptikon, RRID:SCR_008369)Janelia Research Last checked downnif-0000-32983
V3DResource, segmentation software, image analysis software, data processing software, software application, data visualization software, software resource, d visualization softwareV3D is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions, is Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily. V3D-Neuron is a powerful 3D neuron reconstruction, visualization, and editing software built on top of V3D. Both V3D and V3D-Neuron have recently been published in Nature Biotechnology (April, 2010), and Highlighted in Nature Methods (May, 2010), and Science News (April, 2010), etc. V3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes V3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, V3D streamlines the workflow of visualization-assisted analysis. In the latest V3D development, it can render 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales. It even has a Matlab file IO toolbox. A user can now write his/her own plugins to take advantage of the V3D platform very easily.3d, annotation, bioimage, brain, cell, development, informatics, neuron, registration, segmentation, software, tracing, visual, visualization, imageSCR_008646(V3D, RRID:SCR_008646)Janelia Research Howard Hughes Medical InstitutePMID:20231818Last checked upnif-0000-32975
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