Raza, Shan-e-Ahmed, Humayun, Ahmad, Abouna, Sylvie, Nattkemper, Tim W., Epstein, David B. A., Khan, Michael and Rajpoot, Nasir M. (Nasir Mahmood). (2012) RAMTaB : robust alignment of multi-tag bioimages. PLoS One, Vol.7 (No.2). e30894. ISSN 1932-6203

Preview

Text WRAP_Raza_RAMTaB_Robust_alignment.pdf - Published Version Available under License Creative Commons Attribution. Download (3094Kb) | Preview

Abstract

For the discovery of protein complexes and of functional protein networks within a cell, alignment of the tag images in a multi-tag fluorescence image stack is a key pre-processing step. The proposed framework is shown to produce accurate alignment results on both real and synthetic data. Our future work will use the aligned multi-channel fluorescence image data for normal and diseased tissue specimens to analyze molecular co-expression patterns and functional protein networks.

Item Type:	Journal Article
Subjects:	Q Science > QH Natural history
Divisions:	Faculty of Science > Computer Science Faculty of Science > Life Sciences (2010- ) Faculty of Science > Mathematics
Library of Congress Subject Headings (LCSH):	Imaging systems in biology -- Methodology
Journal or Publication Title:	PLoS One
Publisher:	Public Library of Science
ISSN:	1932-6203
Date:	8 February 2012
Volume:	Vol.7
Number:	No.2
Page Range:	e30894
Identification Number:	10.1371/journal.pone.0030894
Status:	Peer Reviewed
Publication Status:	Published
Access rights to Published version:	Restricted or Subscription Access
Funder:	University of Warwick. Dept. of Computer Science, University of Warwick. Institute of Advanced Study
Grant number:	IAIC1003 (IAS)
References:	1. Peng H (2008) Bioimage Informatics: a new area of engineering biology. Bioinformatics 24: 1827–1836. 2. Swedlow JR, Goldberg IG, Eliceiri KW (2009) Bioimage informatics for experimental biology. Annual Review of Biophysics 38: 327–346. 3. Swedlow JR, Eliceiri KW (2009) Open source bioimage informatics for cell biology. Trends in Cell Biology 19: 656–660. 4. Megason SG, Fraser SE (2007) Imaging in systems biology. Cell 130: 784–795. 5. Starkuviene V, Pepperkok R (2007) The potential of high-content highthroughput microscopy in drug discovery. British Journal of Pharmacology 152: 62–71. 6. Verveer PJ, Bastiaens PIH (2008) Quantitative microscopy and systems biology: seeing the whole picture. Histochemistry and Cell Biology 130: 833–843. 7. Cornett DS, Reyzer ML, Chaurand P, Caprioli RM (2007) MALDI imaging mass spectrometry: molecular snapshots of biochemical systems. Nature Methods 4: 828–833. 8. Van Manen H-J, Kraan YM, Roos D, Otto C (2005) Single-cell Raman and fluorescence microscopy reveal the association of lipid bodies with phagosomes in leukocytes. Proceedings of the National Academy of Sciences of the United States of America 102: 10159–10164. 9. Can A, Bello M, Cline H, Tao X, Ginty F, et al. (2008) Multi-modal imaging of histological tissue sections. In: International Symposium on Biomedical Imaging. Paris: IEEE. pp 288–291. 10. Barash E, Dinn S, Sevinsky C, Ginty F (2010) Multiplexed analysis of proteins in tissue using multispectral fluorescence imaging. IEEE Transactions on Medical Imaging 29: 1457–1462. 11. Schubert W, Bonnekoh B, Pommer AJ, Philipsen L, Bo¨ckelmann R, et al. (2006) Analyzing proteome topology and function by automated multidimensional fluorescence microscopy. Nature Biotechnology 24: 1270–1278. 12. Bode M, Krusche A (2007) Toponome Imaging System (TIS): imaging the proteome with functional resolution. Nature Methods Application Notes 4: 1–2. 13. Herold J, Zhou L, Abouna S, Pelengaris S, Epstein D, et al. (2010) Integrating semantic annotation and information visualization for the analysis of multichannel fluorescence micrographs from pancreatic tissue. Computerized Medical Imaging and Graphics 34: 446–452. 14. Herold J, Loyek C, Nattkemper TW (2011) Multivariate image mining. Data Mining and Knowledge Discovery 1: 2–13. 15. Langenka¨mper D, Ko¨lling J, Humayun A, Abouna S, Epstein D, et al. (2011) Towards protein network analysis using TIS imaging and exploratory data analysis. In: Proceedings Workshop on Computational Systems Biology (WCSB). Zurich, . 16. Zitova B (2003) Image registration methods: a survey. Image and Vision Computing 21: 977–1000. 17. Pluim JPW, Maintz JBA, Viergever MA (2003) Mutual-information-based registration of medical images: a survey. IEEE Transactions on Medical Imaging 22: 986–1004. 18. Maintz JB, Viergever MA (1998) A survey of medical image registration. Medical Image Analysis 2: 1–36. 19. Salvi J, Matabosch C, Fofi D, Forest J (2007) A review of recent range image registration methods with accuracy evaluation. Image and Vision Computing 25: 578–596. 20. Chen H-M, Varshney PK (2003) Mutual information-based CT-MR brain image registration using generalized partial volume joint histogram estimation. IEEE Transactions on Medical Imaging 22: 1111–1119. 21. Wells WM, Viola P, Atsumi H, Nakajima S, Kikinis R (1996) Multi-modal volume registration by maximization of mutual information. Medical Image Analysis 1: 35–51. 22. Maes F, Collignon A, Vandermeulen D, Marchal G, Suetens P (1997) Multimodality image registration by maximization of mutual information. IEEE Transactions on Medical Imaging 16: 187–198. 23. Lu X, Zhang S, Su H, Chen Y (2008) Mutual information-based multimodal image registration using a novel joint histogram estimation. Computerized Medical Imaging and Graphics 32: 202–209. 24. Rohde GK, Pajevic S, Pierpaoli C, Basser PJ (2003) A Comprehensive Approach for Multi-channel Image Registration. Biomedical Image Registration. pp 214–223. 25. Rohde GK, Pajevic S, Pierpaoli C (2004) Multi-channel registration of diffusion tensor images using directional information. International Symposium on Biomedical Imaging. pp 712–715. 26. Li Y, Verma R (2011) Multichannel image registration by feature-based information fusion. IEEE Transactions on Medical Imaging 30: 707–720. 27. Rieger B, Molenaar C, Dirks RW, Van Vliet LJ (2004) Alignment of the cell nucleus from labeled proteins only for 4D in vivo imaging. Microscopy Research and Technique 64: 142–150. 28. Wilson CA, Theriot JA (2006) A correlation-based approach to calculate rotation and translation of moving cells. IEEE Transactions on Image Processing 15: 1939–1951. 29. Matula P, Matula P, Kozubek M, Dvora´k V (2006) Fast point-based 3-D alignment of live cells. IEEE Transactions on Image Processing 15: 2388–2396. 30. Wang YP (2004) M-FISH image registration and classification. In: Biomedical Imaging Nano to Macro 2004 IEEE International Symposium on IEEE. pp 57–60. 31. Kim I, Yang S, Baccon P, Heard E, Chen YC, et al. (2007) Non-rigid temporal registration of 2d and 3d multi-channel microscopy image sequences of human cells. Biomedical Imaging From Nano to Macro 2007 ISBI 2007 4th IEEE International Symposium on. pp 1328–1331. 32. Thirion JP (1998) Image matching as a diffusion process: an analogy with Maxwell’s demons. Medical Image Analysis 2: 243–260. 33. Gonzalez RC, Woods RE (2008) Digital Image Processing. New Jersey: Pearson Education. 34. Bhattacharya S, Mathew G, Ruban E, Epstein DBA, Krusche A, et al. (2010) 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. Journal of Proteome Research 9: 6112–6125. 35. Murphy RF (2006) Putting proteins on the map. Nature Biotechnology 24: 1223–1224. 36. Friedenberger M, Bode M, Krusche A, Schubert W (2007) Fluorescence detection of protein clusters in individual cells and tissue sections by using toponome imaging system: sample preparation and measuring procedures. Nature Protocols 2: 2285–2294. 37. Schubert W, Gieseler A, Krusche A (2009) Mapping in prostate cancer: detection of 2000 cell surface protein clusters in a single tissue section and cell type specific annotation by using a three symbol code. Journal of Proteome Research 8: 2696–2707. 38. Bhattacharya S (2011) Identification of colon cancer specific protein clusters by toponome imaging system and their cellular annotation by using a three symbol code. University of Warwick. 39. Yang S, Kohler D, Teller K, Cremer T, Le Baccon P, et al. (2008) Nonrigid registration of 3-d multichannel microscopy images of cell nuclei. IEEE Transactions on Image Processing 17: 493–499. 40. Likar B (2001) A hierarchical approach to elastic registration based on mutual information. Image and Vision Computing 19: 33–44. 41. Audet C, Dennis JE (2002) Analysis of Generalized Pattern Searches. SIAM Journal on Optimization 13: 889. 42. Kolda TG, Lewis RM, Torczon V (2006) A generating set direct search augmented Lagrangian algorithm for optimization with a combination of general and linear constraints. Sandia National Laboratories. 43. Keys RG (1981) Cubic convolution interpolation for digital image processing. IEEE Transactions on Acoustics Speech and Signal Processing 29: 1153–1160.
URI:	http://wrap.warwick.ac.uk/id/eprint/42294

Request changes to a record

Actions (login required)

View Item