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ClearVolume

ClearVolume is a real-time live 3D visualization library designed for high-end volumetric microscopes such as SPIM and DLSM microscopes. With ClearVolume you can see live on your screen the stacks acquired by your microscope instead of waiting for offline post-processing to give you an intuitive and comprehensive view on your data. The biologists can immediately decide whether a sample is worth imaging.ClearVolume can easily be integrated into existing Java, C/C++, Python, or LabVIEW based microscope software. It has a dedicated interface to MicroManager/OpenSpim/OpenSpin control software. ClearVolume supports multi-channels, live 3D data streaming from remote microscopes, and uses a multi-pass Fibonacci rendering algorithm that can handle large volumes. Moreover, ClearVolume is integrated into the Fiji/ImageJ2/KNIME ecosystem. You can now open your stacks with ClearVolume from within these popular frameworks for offline viewing.

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Institution: Center for Systems Biology & Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany; Technische Universität Dresden, Dresden, Germany

EpiTools

EpiTools provides user-friendly graphical user interfaces for accurately segmenting and tracking the contours of cell membrane signals obtained from 4D confocal imaging. It is designed for a broad audience, especially biologists with no computer-science background. Quantitative data extraction is integrated into a larger bioimaging platform, Icy, to increase the visibility and usability of thetools.

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Institution: UZH, Zurich, Switzerland; ZHAW, Zurich, Switzerland; SIB, Lausanne, Switzerland; UCL, London, United Kingdom; Kingston University, Kingston, United Kingdom; Cancer Research UK, London, United Kingdom

SynTView

SynTView is a recently published interactive multi-view genome browser for next-generation comparative microorganism genomics. The software is characterised by the presentation of syntenic organisations of microbial genomes and the visualisation of polymorphism data obtained from next generation sequencing. SynTView is built as a generic genome browser including sub-maps that hold information about genomic objects. After selecting genomes of interest, the users can explore them visually by genomic location, or directly go to specific genes by name. Several genomic maps can be stacked on top of each other. The creation of a SynTView website is very helpful in the analysis of a large number of strains, bringing together phylogeny, polymorphisms, larger variants such as indels, coverage, as well as functional annotations and strains meta-data. SynTView is designed to visualise information about polymorphism across a large number of bacterial strains. The SNP maps allow the user to navigate through polymorphism data sets. SynTView has been integrated to the Listeriomics web site, a platform for visualizing and analysing every heterogeneous Listeria "omics" dataset published to date.

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Institution: Institut Pasteur, Paris, France

MegaMol

MegaMol™ is a visualization middleware used to visualize point-based molecular datasets.

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Institution: ​Visualization Research Center (VISUS) of the University of Stuttgart, Germany

MegaMol™ is a visualization middleware used to visualize point-based molecular datasets. This software is developed within the Collaborative Research Center 716, subproject D.3 at the Visualization Research Center (VISUS) of the University of Stuttgart and at the Computer Graphics and Visualization Group of the TU Dresden.

BioJS

BioJS is a library of over hundred JavaScript components enabling you to visualize and process data using current web technologies.

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Institution: BioJS

eHistology Atlas

The eHistology Atlas is a Javascript-based zoom viewer of large 2D histology images with anatomy annotations provided via point locations that can be selected to show additional imformation. The tiled images are provided by an Image Internet Protocol (IIP) server and the anatomy annotations from a mySQL database. All software is available from the matech GitHub repository https://github.com/ma-tech. The browser code is Javascript and tested on Firefox, Chrome and Safari. The eMouseAtlas resource provide access to the eHistology Atlas.

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Institution: MRC Human Genetics Unit, University of Edinburgh

Integrated Genome Browser

The Integrated Genome Browser (IGB, pronounced Ig-Bee) is a fast, flexible, and free desktop genome browser. First developed at Affymetrix in 2001 to support visual analytics of genome tiling arrays, IGB provides an advanced, highly customizable environment for exploring and analyzing large-scale genomic data sets.

Using IGB, you can:

  • View your RNA-Seq, ChIP-chip or ChIP-seq data alongside genome annotations and sequence.
  • Investigate alternative splicing, regulation of gene expression, epigenetic modifications of DNA, and other genome-scale questions.
  • View results from aligning short-read sequences onto a target genome, identify SNPs, and check alignment quality.
  • Copy and paste genomic sequences for further analysis into other tools, such as primer design and promoter analysis tools.
  • Create high-quality images for publication in a variety of formats.

 

IGB features

IGB lets you view results from your own experiments or computational analyses alongside public domain gene annotations, sequences, and genomic data sets, thus making it easier for you to determine how your experiments agree or disagree with current thinking and models of genomic structure.

Some features IGB offers include:

  • Animated zooming. Most genome browsers implement "jump zooming" only, in which you click a zoom button (or other type of control) and then wait for the display to re-draw. In IGB, zooming is animated, allowing you to easily and quickly adjust the zoom level as needed without losing track of your location.
  • Simple Data Sharing System - QuickLoad. IGB implements a very simple, easy-to-use system for sharing data called QuickLoad. You can use the QuickLoad system to set up a Web site you can use to share your data with colleagues, reviewers, and the public.
  • Draggable graphs. You can display genome graphs data (e.g., "bar" and "wiggle" files) alongside and even on top of reference genome annotations, thus making it easier to see how your experimental results match up to the published reference genome annotations. You can reset your graphs to "floating" and click-drag them over annotations to compare your results with annotations and others' experiments.
  • Edge-matching across tracks. When you click an item in the display, the edges of other items in the same or different tracks with identical boundaries light up, highlighting interesting similarities or differences across gene models, sequence reads, or other features.
  • Integration with local and remote external data sources. IGB can load data from a variety of sources, including Distributed Annotation Servers, QuickLoad servers, ordinary Web sites, and local files.
  • Intron-trimming sliced view. In many species, introns are huge when compared to the exonic (coding) regions of genes. IGB provides a Sliced View tab that trims uninformative regions from introns.
  • Web-controls. IGB can be controlled from a web browser or any other program capable of sending HTTP requests. Via IGB links, you can create Web pages that direct IGB to scroll to a specific region and load data sets from local files or servers.
  • Scripting. IGB understands a simple command language that allows users to write simple scripts directing IGB to show a genome, zoom and scroll to specific regions, and other functions.
  • Open source. All development on IGB proceeds via a 100% open source model. The license allows developers to incorporate IGB (and its components) into new applications.
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Institution: UNC @ Charlotte

GraphiteLifeExplorer

The GraphiteLifeExplorer modeling tool allows to build 3D molecular assemblies of proteins and DNA from Protein Database (PDB) files. Atomic DNA can be modeled from scratch or reconstructed from simulation.

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Institution: Fourmentin-Guilbert Scientific Foundation & Inria

The LifeExplorer initiative aims at providing a multiscale modelisation of a complete bacteria.

One software is currently available: GraphiteLifeExplorer

OMERO

From the microscope to publication, OMERO handles all your images in a secure central repository. You can view, organize, analyze and share your data from anywhere you have internet access. Work with your images from a desktop app (Windows, Mac or Linux), from the web or from 3rd party software. Over 130 image file formats supported, including all major microscope formats.

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Institution: University of Dundee

http://www.openmicroscopy.org/site/about/development-teams/jason

Aequatus

We present the Aequatus, a web-based tool with novel rendering approaches to visualise homologous, orthologous and paralogous gene structures among differing species or subtypes of a common species. The Aequatus utilises web technologies to provide a fast and intuitive browsing experience over complex comparative data. The Aequatus processes and visualises data directly from the Ensembl Compara and Ensembl Core schema databases by using precalculated genomic alignments from Ensembl Compara and relating them to Ensembl Core to gather genomic feature information, visualising phylogenetic and structural relationships among them via CIGAR strings. Whilst applicable to species with high-quality gold-standard reference genomes such as human or mouse, the Aequatus was designed with large fragmented genome references in mind,  e.g. polyploid plants. The ultimate goal of the Aequatus is to provide a unique and informative way to render and explore complex relationships between genes from various species.

Source Code: https://github.com/TGAC/Aequatus

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Institution: Earlham Institute

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