Dataset Information

WHIDE--a web tool for visual data mining colocation patterns in multivariate bioimages.

ABSTRACT:

Motivation

Bioimaging techniques rapidly develop toward higher resolution and dimension. The increase in dimension is achieved by different techniques such as multitag fluorescence imaging, Matrix Assisted Laser Desorption / Ionization (MALDI) imaging or Raman imaging, which record for each pixel an N-dimensional intensity array, representing local abundances of molecules, residues or interaction patterns. The analysis of such multivariate bioimages (MBIs) calls for new approaches to support users in the analysis of both feature domains: space (i.e. sample morphology) and molecular colocation or interaction. In this article, we present our approach WHIDE (Web-based Hyperbolic Image Data Explorer) that combines principles from computational learning, dimension reduction and visualization in a free web application.

Results

We applied WHIDE to a set of MBI recorded using the multitag fluorescence imaging Toponome Imaging System. The MBI show field of view in tissue sections from a colon cancer study and we compare tissue from normal/healthy colon with tissue classified as tumor. Our results show, that WHIDE efficiently reduces the complexity of the data by mapping each of the pixels to a cluster, referred to as Molecular Co-Expression Phenotypes and provides a structural basis for a sophisticated multimodal visualization, which combines topology preserving pseudocoloring with information visualization. The wide range of WHIDE's applicability is demonstrated with examples from toponome imaging, high content screens and MALDI imaging (shown in the Supplementary Material).

Availability and implementation

The WHIDE tool can be accessed via the BioIMAX website http://ani.cebitec.uni-bielefeld.de/BioIMAX/; Login: whidetestuser; Password: whidetest.

SUBMITTER: Kolling J

PROVIDER: S-EPMC3324520 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature

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Publications

WHIDE--a web tool for visual data mining colocation patterns in multivariate bioimages.

Kölling Jan J Langenkämper Daniel D Abouna Sylvie S Khan Michael M Nattkemper Tim W TW

Bioinformatics (Oxford, England) 20120305 8

<h4>Motivation</h4>Bioimaging techniques rapidly develop toward higher resolution and dimension. The increase in dimension is achieved by different techniques such as multitag fluorescence imaging, Matrix Assisted Laser Desorption / Ionization (MALDI) imaging or Raman imaging, which record for each pixel an N-dimensional intensity array, representing local abundances of molecules, residues or interaction patterns. The analysis of such multivariate bioimages (MBIs) calls for new approaches to sup ...[more]

PMID: 22390938

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Dataset Information

WHIDE--a web tool for visual data mining colocation patterns in multivariate bioimages.

Motivation

Results

Availability and implementation

Publications

WHIDE--a web tool for visual data mining colocation patterns in multivariate bioimages.

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