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Protocols

VisBio specifications

Information


Unique identifier OMICS_13520
Name VisBio
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data A diversity of biological file formats using the Bio-Formats library
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Version 3.40
Stability Stable
Requirements
Java3D
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Kevin Eliceiri

Publications for VisBio

VisBio citations

 (3)
library_books

IQM: An Extensible and Portable Open Source Application for Image and Signal Analysis in Java

2015
PLoS One
PMCID: 4303421
PMID: 25612319
DOI: 10.1371/journal.pone.0116329

[…] tissue can be automated with the software toolkit TMARKER (current version: v1.20614, Java), which uses machine learning algorithms based on randomized decision trees and support vector machines []. VisBio, loci.wisc.edu/software/visbio:The software tool VisBio (current version: 3.40rc1, Java) can be used for visualization of high-dimensional image data and its analysis. Its special focus is on t […]

call_split

Collagen density promotes mammary tumor initiation and progression

2008
PMCID: 2386807
PMID: 18442412
DOI: 10.1186/1741-7015-6-11
call_split See protocol

[…] are acquisition package developed at LOCI (Laboratory for Optical and Computational Instrumentation, University of Wisconsin, Madison, WI) and image analysis for MPE/SHG was performed with ImageJ and VisBio [] software. For TACS-1 image analysis, additional surface rendering plug-ins for ImageJ were utilized []. For TACS-2 and -3, ImageJ was used to quantify the collagen fiber angle relative to th […]

call_split

Collagen reorganization at the tumor stromal interface facilitates local invasion

2006
PMCID: 1781458
PMID: 17190588
DOI: 10.1186/1741-7015-4-38
call_split See protocol

[…] n package developed at LOCI (Laboratory for Optical and Computational Instrumentation, University of Wisconsin, Madison, WI, USA). Image analysis for combined MPE-SHG was performed with ImageJ [] and VisBio [] software. Using ImageJ, differences in collagen density were quantified by measuring the area of collagen signal following density slicing from a constant threshold, and local and mean inten […]

Citations

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VisBio institution(s)
Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, Madison, WI, USA
VisBio funding source(s)
National Institutes of Health (NIH) National Institute of Biomedical Imaging and BioEngineering (NIBIB) grant no. EB10084

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