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.

Download
OA
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Volltext vorhanden für diesen Nachweis
Abstract / Bemerkung
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).
Erscheinungsjahr
Zeitschriftentitel
Bioinformatics
Band
28
Zeitschriftennummer
8
Seite
1143-1150
ISSN
eISSN
PUB-ID

Zitieren

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. doi:10.1093/bioinformatics/bts104
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.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
This Item is protected by copyright and/or related rights. [...]
Volltext(e)
Access Level
OA Open Access
Zuletzt Hochgeladen
2016-11-24T14:48:45Z

Link(s) zu Volltext(en)
Access Level
Restricted Closed Access

10 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Spatio-Temporal Metabolite Profiling of the Barley Germination Process by MALDI MS Imaging.
Gorzolka K, Kölling J, Nattkemper TW, Niehaus K., PLoS One 11(3), 2016
PMID: 26938880
Robust normalization protocols for multiplexed fluorescence bioimage analysis.
Ahmed Raza SE, Langenkämper D, Sirinukunwattana K, Epstein D, Nattkemper TW, Rajpoot NM., BioData Min 9(), 2016
PMID: 26949415
Predicate Oriented Pattern Analysis for Biomedical Knowledge Discovery.
Shen F, Liu H, Sohn S, Larson DW, Lee Y., Intell Inf Manag 8(3), 2016
PMID: 28983419
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
Fully automated registration of vibrational microspectroscopic images in histologically stained tissue sections.
Yang C, Niedieker D, Grosserüschkamp F, Horn M, Tannapfel A, Kallenbach-Thieltges A, Gerwert K, Mosig A., BMC Bioinformatics 16(), 2015
PMID: 26607812
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
Biological Interpretation of Morphological Patterns in Histopathological Whole-Slide Images.
Kothari S, Phan JH, Osunkoya AO, Wang MD., ACM BCB 2012(), 2012
PMID: 29568817

27 References

Daten bereitgestellt von Europe PubMed Central.

Spatial segmentation of imaging mass spectrometry data with edge-preserving image denoising and clustering.
Alexandrov T, Becker M, Deininger SO, Ernst G, Wehder L, Grasmair M, von Eggeling F, Thiele H, Maass P., J. Proteome Res. 9(12), 2010
PMID: 20954702
Toponome imaging system: in situ protein network mapping in normal and cancerous colon from the same patient reveals more than five-thousand cancer specific protein clusters and their subcellular annotation by using a three symbol code
Bhattacharya S.., 2010

Chambers J.M.., 1983
The use of faces to represent points in k-dimensional space graphically
Chernoff H.., 1973
MALDI imaging mass spectrometry: molecular snapshots of biochemical systems.
Cornett DS, Reyzer ML, Chaurand P, Caprioli RM., Nat. Methods 4(10), 2007
PMID: 17901873
Comparative in situ topoproteome analysis reveals differences in patch test-induced eczema: cytotoxicity-dominated nickel versus pleiotrope pollen reaction.
Eyerich K, Bockelmann R, Pommer AJ, Foerster S, Hofmeister H, Huss-Marp J, Cavani A, Behrendt H, Ring J, Gollnick H, Bonnekoh B, Traidl-Hoffmann C., Exp. Dermatol. 19(6), 2009
PMID: 19758337
Data mining in multivariate images
Herold J.., 2011
A focus+content technique based on hyperbolic geometry for viewing large hierarchies
Lamping J.., 1995
Tical - a web-tool for multivariate image clustering and data topology preserving visualization
Langenkämper D.., 2011
Exploring n-dimensional databases
LeBlanc J.., 1990
Color icons: Merging color and texture perception for integrated visualization of multiple parameters
Levkovitz H.., 1991
BioIMAX: a Web 2.0 approach for easy exploratory and collaborative access to multivariate bioimage data.
Loyek C, Rajpoot NM, Khan M, Nattkemper TW., BMC Bioinformatics 12(), 2011
PMID: 21777450
Imaging in systems biology.
Megason SG, Fraser SE., Cell 130(5), 2007
PMID: 17803903
Large-scale data exploration with the hierarchically growing hyperbolic SOM.
Ontrup J, Ritter H., Neural Netw 19(6-7), 2006
PMID: 16806818
Iconographic displays for visualizing multidimensional data
Pickett R.M., Grinstein G.G.., 1988
RAMTaB: robust alignment of multi-tag bioimages
Raza S.A.., 2012
In situ localization of epidermal stem cells using a novel multi epitope ligand cartography approach.
Ruetze M, Gallinat S, Wenck H, Deppert W, Knott A., Integr Biol (Camb) 2(5-6), 2010
PMID: 20535415
The eyes have it: a task by data type taxonomy for information visualizations
Schneiderman B.., 1996
Sequence logos: a new way to display consensus sequences.
Schneider TD, Stephens RM., Nucleic Acids Res. 18(20), 1990
PMID: 2172928
Analyzing proteome topology and function by automated multidimensional fluorescence microscopy.
Schubert W, Bonnekoh B, Pommer AJ, Philipsen L, Bockelmann R, Malykh Y, Gollnick H, Friedenberger M, Bode M, Dress AW., Nat. Biotechnol. 24(10), 2006
PMID: 17013374
The potential of high-content high-throughput microscopy in drug discovery.
Starkuviene V, Pepperkok R., Br. J. Pharmacol. 152(1), 2007
PMID: 17603554
Bilateral filtering for gray and color images
Tomasi C., Manduchi R.., 1998
Single-cell Raman and fluorescence microscopy reveal the association of lipid bodies with phagosomes in leukocytes.
van Manen HJ, Kraan YM, Roos D, Otto C., Proc. Natl. Acad. Sci. U.S.A. 102(29), 2005
PMID: 16002471
Neighborhood preservation in nonlinear projection methods: an experimental study
Venna J., Kaski S.., 2001

Ware C.., 2004

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 22390938
PubMed | Europe PMC

Suchen in

Google Scholar