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

Kölling J, Langenkämper D, Sylvie A, Michale K, Nattkemper TW (2012)
Bioinformatics 28(8): 1143-1150.

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Motivation: Bioimaging techniques rapidly develop towards higher resolution and dimension. The increase in dimension is achieved by different techniques such as multi-tag fluorescence imaging, MALDI imaging or Raman imaging, which record for each pixel a N dimensional intensity array, representing local abundances of molecules, residues or interaction patterns. The analysis of such multivariate bioimages (MBI) 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 paper 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 multi-tag fluorescence imaging TIS (Toponome Imaging System). The MBI show FOV 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 MCEP (Molecular Co-Expression Phenotypes) and provides a structural basis for a sophisticated multi-modal 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).
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Kölling J, Langenkämper D, Sylvie A, Michale K, Nattkemper TW. WHIDE - A web tool for visual data mining colocation patterns in multivariate bioimages. Bioinformatics. 2012;28(8):1143-1150.
Kölling, J., Langenkämper, D., Sylvie, A., Michale, K., & Nattkemper, T. W. (2012). WHIDE - A web tool for visual data mining colocation patterns in multivariate bioimages. Bioinformatics, 28(8), 1143-1150.
Kölling, J., Langenkämper, D., Sylvie, A., Michale, K., and Nattkemper, T. W. (2012). WHIDE - A web tool for visual data mining colocation patterns in multivariate bioimages. Bioinformatics 28, 1143-1150.
Kölling, J., et al., 2012. WHIDE - A web tool for visual data mining colocation patterns in multivariate bioimages. Bioinformatics, 28(8), p 1143-1150.
J. Kölling, et al., “WHIDE - A web tool for visual data mining colocation patterns in multivariate bioimages”, Bioinformatics, vol. 28, 2012, pp. 1143-1150.
Kölling, J., Langenkämper, D., Sylvie, A., Michale, K., Nattkemper, T.W.: WHIDE - A web tool for visual data mining colocation patterns in multivariate bioimages. Bioinformatics. 28, 1143-1150 (2012).
Kölling, Jan, Langenkämper, Daniel, Sylvie, Abouna, Michale, Khan, and Nattkemper, Tim Wilhelm. “WHIDE - A web tool for visual data mining colocation patterns in multivariate bioimages”. Bioinformatics 28.8 (2012): 1143-1150.
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6 Citations in Europe PMC

Data provided by Europe PubMed Central.

Robust normalization protocols for multiplexed fluorescence bioimage analysis.
Ahmed Raza SE, Langenkamper D, Sirinukunwattana K, Epstein D, Nattkemper TW, Rajpoot NM., BioData Min 9(), 2016
PMID: 26949415
Spatio-Temporal Metabolite Profiling of the Barley Germination Process by MALDI MS Imaging.
Gorzolka K, Kolling J, Nattkemper TW, Niehaus K., PLoS ONE 11(3), 2016
PMID: 26938880
Fully automated registration of vibrational microspectroscopic images in histologically stained tissue sections.
Yang C, Niedieker D, Grosseruschkamp F, Horn M, Tannapfel A, Kallenbach-Thieltges A, Gerwert K, Mosig A., BMC Bioinformatics 16(), 2015
PMID: 26607812
Colocalization of fluorescence and Raman microscopic images for the identification of subcellular compartments: a validation study.
Krauß SD, Petersen D, Niedieker D, Fricke I, Freier E, El-Mashtoly SF, Gerwert K, Mosig A., Analyst 140(7), 2015
PMID: 25679809
DiSWOP: a novel measure for cell-level protein network analysis in localized proteomics image data.
Kovacheva VN, Khan AM, Khan M, Epstein DB, Rajpoot NM., Bioinformatics 30(3), 2014
PMID: 24273247

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