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on page 1 showing 20 out of 452 results

Cite this (3D Interactive Chemical Shift Imaging, RRID:SCR_002581)

URL: https://www.nitrc.org/projects/threedicsi/

Resource Type: Resource, software resource, software application, data processing software

A user-friendly and comprehensive software program for multi-dimensional CSI data visualization, spectral processing, localization, quantification and multi-variate analysis.

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Cite this (3D Slicer, RRID:SCR_005619)

URL: http://slicer.org/

Resource Type: Resource, data visualization software, software application, data processing software, image analysis software, software resource

A free, open source software package for visualization and image analysis including registration, segmentation, and quantification of medical image data. Slicer provides a graphical user interface to a powerful set of tools so they can be used by end-user clinicians and researchers alike. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X. Slicer is based on VTK (http://public.kitware.com/vtk) and has a modular architecture for easy addition of new functionality. It uses an XML-based file format called MRML - Medical Reality Markup Language which can be used as an interchange format among medical imaging applications. Slicer is primarily written in C++ and Tcl.

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Cite this (3DViewnix, RRID:SCR_007351)

URL: http://mipgsun.mipg.upenn.edu/~Vnews/

Resource Type: Resource, software resource, software application, data processing software, d visualization software

Data-, machine-, and application- independent software system for the visualization and analysis of multidimensional images. This transportable, very inexpensive software system, has capabilities for visualizing, manipulating, and analyzing multidimensional, multimodality image information. It is designed to run on Unix machines under X-windows. It uses a data protocol that is a multidimensional generalization of the ACR-NEMA standards. We have tested it extensively on SGI and Sun workstations and PCs. Other recipients of 3DVIEWNIX have installed it on a variety of platforms including IBM RS6000s, HP700s, and Stardent, all from a single source code version. UNIQUE FEATURES OF 3DVIEWNIX * Transportable - based on UNIX, X-window, and C * Based on multidimensional generalization of ACR-NEMA standards of data representation * Application-independent * Image dimensionality independent * Can handle rigid, non-rigid, static, and dynamic objects and object assemblies * Can handle object information from multiple modalities and longitudinal acquisitions * Multitudes of visualization, manipulation, and analysis methods incorporated * Open software system distributed with source code

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    aBEAT

Cite this (aBEAT, RRID:SCR_002238)

URL: http://www.med.unc.edu/bric/ideagroup/free-softwares/abeat-a-toolbox-for-consistent-analysis-of-longitudinal-adult-brain-mri

Resource Type: Resource, image analysis software, data processing software, software application, software resource, software toolkit, image processing software

A 4D adult brain extraction and analysis toolbox with graphical user interfaces to consistently analyze 4D adult brain MR images. Single-time-point images can also be analyzed. Main functions of the software include image preprocessing, 4D brain extraction, 4D tissue segmentation, 4D brain labeling, ROI analysis. Linux operating system (64 bit) is required. A computer with 8G memory (or more) is recommended for processing many images simultaneously. The graphical user interfaces and overall framework of the software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing.

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Cite this (Advanced 3D Visualization and Volume Modeling, RRID:SCR_007353)

URL: http://www.fei.com/software/amira-3d-for-life-sciences/

Resource Type: Resource, data analysis software, data processing software, software application, data visualization software, 3d visualization software, software resource

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.

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Cite this (Advanced Neuroscience Imaging Research Laboratory Software Packages, RRID:SCR_002926)

URL: http://www.fmri.wfubmc.edu/cms/software

Resource Type: Resource, software resource, software toolkit

Research group based in the Department of Radiology of Wake Forest University School of Medicine devoted to the application of novel image analysis methods to research studies. The ANSIR lab also maintains a fully-automated functional and structural image processing pipeline supporting the image storage and analysis needs of a variety of scientists and imaging studies at Wake Forest. Software packages and toolkits are currently available for download from the ANSIR Laboratory, including: WFU Biological Parametric Mapping Toolbox, WFU_PickAtlas, and Adaptive Staircase Procedure for E-Prime.

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Cite this (AffyExpress, RRID:SCR_001321)

URL: http://www.bioconductor.org/packages/release/bioc/html/AffyExpress.html

Resource Type: Resource, software resource

Software package for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.

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    agriGO

Cite this (agriGO, RRID:SCR_006989)

URL: http://bioinfo.cau.edu.cn/agriGO/

Resource Type: Resource, data analysis service, database, analysis service resource, production service resource, service resource, data or information resource

A web-based tool and database for the gene ontology analysis. Its focus is on agricultural species and is user-friendly. The agriGO is designed to provide deep support to agricultural community in the realm of ontology analysis. Compared to other available GO analysis tools, unique advantages and features of agriGO are: # The agriGO especially focuses on agricultural species. It supports 45 species and 292 datatypes currently. And agriGO is designed as an user-friendly web server. # New tools including PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross comparison of SEA) were developed. The arrival of these tools provides users with possibilities for data mining and systematic result exploration and will allow better data analysis and interpretation. # The exploratory capability and result visualization are enhanced. Results are provided in different formats: HTML tables, tabulated text files, hierarchical tree graphs, and flash bar graphs. # In agriGO, PAGE and SEACOMPARE can be used to carry out cross-comparisons of results derived from different data sets, which is very important when studying multiple groups of experiments, such as in time-course research. Platform: Online tool

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Cite this (Algal Functional Annotation Tool, RRID:SCR_012034)

URL: http://pathways.mcdb.ucla.edu/algal/

Resource Type: Resource, data analysis service, database, analysis service resource, production service resource, service resource, data or information resource

Tools to search gene lists for functional term enrichment as well as to dynamically visualize proteins onto pathway maps. Additionally, integrated expression data may be used to discover similarly expressed genes based on a starting gene of interest.

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Cite this (Allen Human Brain Atlas, RRID:SCR_007416)

URL: http://human.brain-map.org/

Resource Type: Resource, data processing software, database, software application, data visualization software, software resource, atlas, data or information resource

Multi modal atlas of human brain that integrates anatomic and genomic information, coupled with a suite of visualization and mining tools to create an open public resource for brain researchers and other scientists. Data include magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), histology and gene expression data derived from both microarray and in situ hybridization (ISH) approaches. Brain Explorer 2 is a desktop software application for viewing the human brain anatomy and gene expression data in 3D. It is available for download.

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    AMILab

Cite this (AMILab, RRID:SCR_009525)

URL: http://amilab.org

Resource Type: Resource, software resource, software application, data processing software

An opensource software for image analysis, processing and visualization. It provides convenient visualization tools for 2D and 3D images and it is highly extensible through its own scripting language. At visualization level, AMILab includes a 2D/3D image viewer, a 3D polygon viewer based on OpenGL, a 2D Curve viewer to visualize 2D curves, histograms and color/opacity transfer functions, and a GPU-enabled raycasting script for Volume Rendering based on VTK. The software includes an automatic C++ wrapping system which permits fast development of new visualization tools and image processing algorithms. This wrapping system currently wraps about 200 classes from wxwidgets library and about 100 classes from VTK.

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Cite this (Analysis of Functional NeuroImages, RRID:SCR_005927)

URL: http://afni.nimh.nih.gov/afni/

Resource Type: Resource, source code, data analysis software, data processing software, software application, data visualization software, software resource, software toolkit

Set of (mostly) C programs that run on X11+Unix-based platforms (Linux, Mac OS X, Solaris, etc.) for processing, analyzing, and displaying functional MRI (FMRI) data defined over 3D volumes and over 2D cortical surface meshes. AFNI is freely distributed as source code plus some precompiled binaries.

  • From Current Category

Cite this (An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application, RRID:SCR_001646)

URL: http://ilyinlab.org/friend/

Resource Type: Resource, data analysis software, data processing software, software application, data visualization software, software resource, rendering software

Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families. Friend is also useful for the functional annotation of proteins, protein modeling, and protein folding studies. Friend provides three levels of usage; 1) an extensive GUI for a scientist with no programming experience, 2) a command line interface for scripting for a scientist with some programming experience, and 3) the ability to extend Friend with user written libraries for an experienced programmer. The application is linked and communicates with local and remote sequence and structure databases.

  • From Current Category

Cite this (ANNOgesic, RRID:SCR_016326)

URL: https://github.com/Sung-Huan/ANNOgesic

Resource Type: Resource, standalone software, data processing software, software application, data analysis software, software resource, software toolkit

Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data.

  • From Current Category

Cite this (ArcGIS for Desktop Basic, RRID:SCR_011081)

URL: http://www.esri.com/software/arcgis/arcgis-for-desktop

Resource Type: Resource, software resource, commercial organization

Geographical information system software produced by Esri.

  • From Current Category

Cite this (aroma.light, RRID:SCR_001312)

URL: http://www.bioconductor.org/packages/release/bioc/html/aroma.light.html

Resource Type: Resource, software resource

Light-weight software package for normalization and visualization of microarray data using only basic R data types. Software can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.

  • From Current Category

Cite this (arrayQuality, RRID:SCR_001315)

URL: http://www.bioconductor.org/packages/release/bioc/html/arrayQuality.html

Resource Type: Resource, software resource

Software functions for performing print-run and array level quality assessment.

  • From Current Category

Cite this (ArrayTools, RRID:SCR_001313)

URL: http://www.bioconductor.org/packages/release/bioc/html/ArrayTools.html

Resource Type: Resource, software resource

Software package for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases.

  • From Current Category

    ascend

Cite this (ascend, RRID:SCR_017257)

URL: https://github.com/powellgenomicslab/ascend

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software R package for analysis of single cell RNA-seq expression, normalization and differential expression data. Provides framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression, and visualization functions.

  • From Current Category

Cite this (Ascidian Network for InSitu Expression and Embryological Data, RRID:SCR_013030)

URL: http://www.aniseed.cnrs.fr/

Resource Type: Resource, database, service resource, storage service resource, software resource, data repository, data or information resource

Database of ascidian embryonic development at the level of the genome (cis-regulatory sequences, gene expression, protein annotation), of the cell (morphology, fate, induction, lineage) or of the whole embryo (anatomy, morphogenesis). Currently, four organism models are described in Aniseed: Ciona intestinalis, Ciona savignyi, Halocynthia roretzi and Phallusia mammillata.
This version supports four sets of Ciona intestinalis transcript models: JGI v1.0, KyotoGrail 2005, KH and ENSEMBL, all functionally annotated, and grouped into Aniseedv3.0 gene models. Users can explore their expression profiles during normal or manipulated development, access validated cis-regulatory regions, get the molecular tools used to assay gene function, or all articles related to the function, or regulation of a given gene. Known transcriptional regulators and targets are listed for each gene, as are the gene regulatory networks acting in individual anatomical territories.
ANISEED is a community tool, and the direct involvement of external contributors is important to optimize the quality of the submitted data. Virtual embryo: The 3D Virtual embryo is available to download in the download section of the website.

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