RAMTaB: Robust Alignment of Multi-Tag Bioimages

Raza S-E-A, Epstein D, Nattkemper TW, Rajpoot N (2012)
PLoS ONE 7(2): e30894.

Download
OA
Zeitschriftenaufsatz | Veröffentlicht | Englisch
Volltext vorhanden für diesen Nachweis
Autor
; ; ;
Abstract / Bemerkung
In recent years, new microscopic imaging techniques have evolved to allow us to visualize several different proteins (or other biomolecules) in a visual field. Analysis of protein co-localization becomes viable because molecules can interact only when they are located close to each other. We present a novel approach to align images in a multi-tag fluorescence image stack. The proposed approach is applicable to multi-tag bioimaging systems which (a) acquire fluorescence images by sequential staining and (b) simultaneously capture a phase contrast image corresponding to each of the fluorescence images. To the best of our knowledge, there is no existing method in the literature, which addresses simultaneous registration of multi-tag bioimages and selection of the reference image in order to maximize the overall overlap between the images.
Erscheinungsjahr
Zeitschriftentitel
PLoS ONE
Band
7
Zeitschriftennummer
2
Seite
e30894
ISSN
eISSN
PUB-ID

Zitieren

Raza S-E-A, Epstein D, Nattkemper TW, Rajpoot N. RAMTaB: Robust Alignment of Multi-Tag Bioimages. PLoS ONE. 2012;7(2):e30894.
Raza, S. - E. - A., Epstein, D., Nattkemper, T. W., & Rajpoot, N. (2012). RAMTaB: Robust Alignment of Multi-Tag Bioimages. PLoS ONE, 7(2), e30894. doi:10.1371/journal.pone.0030894
Raza, S. - E. - A., Epstein, D., Nattkemper, T. W., and Rajpoot, N. (2012). RAMTaB: Robust Alignment of Multi-Tag Bioimages. PLoS ONE 7, e30894.
Raza, S.-E.-A., et al., 2012. RAMTaB: Robust Alignment of Multi-Tag Bioimages. PLoS ONE, 7(2), p e30894.
S.-E.-A. Raza, et al., “RAMTaB: Robust Alignment of Multi-Tag Bioimages”, PLoS ONE, vol. 7, 2012, pp. e30894.
Raza, S.-E.-A., Epstein, D., Nattkemper, T.W., Rajpoot, N.: RAMTaB: Robust Alignment of Multi-Tag Bioimages. PLoS ONE. 7, e30894 (2012).
Raza, Shan-E-Ahmed, Epstein, David, Nattkemper, Tim Wilhelm, and Rajpoot, Nasir. “RAMTaB: Robust Alignment of Multi-Tag Bioimages”. PLoS ONE 7.2 (2012): e30894.
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
2012-03-15T15:26:09Z

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

7 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Non-Rigid Contour-Based Registration of Cell Nuclei in 2-D Live Cell Microscopy Images Using a Dynamic Elasticity Model.
Sorokin DV, Peterlik I, Tektonidis M, Rohr K, Matula P., IEEE Trans Med Imaging 37(1), 2018
PMID: 28783625
Diffeomorphic Multi-Frame Non-Rigid Registration of Cell Nuclei in 2D and 3D Live Cell Images.
Tektonidis M, Rohr K., IEEE Trans Image Process 26(3), 2017
PMID: 28092560
ViCAR: An Adaptive and Landmark-Free Registration of Time Lapse Image Data from Microfluidics Experiments.
Hattab G, Schlüter JP, Becker A, Nattkemper TW., Front Genet 8(), 2017
PMID: 28620411
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
Non-rigid multi-frame registration of cell nuclei in live cell fluorescence microscopy image data.
Tektonidis M, Kim IH, Chen YC, Eils R, Spector DL, Rohr K., Med Image Anal 19(1), 2015
PMID: 25181702
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
Multi-color fluorescence imaging based on plasmonic wavelength selection and double illumination by white light.
Choi JM, Eom K, Hwang S, Lee Y, Jun SB, Byun KM, Kim SJ., Opt Express 22(5), 2014
PMID: 24663934

43 References

Daten bereitgestellt von Europe PubMed Central.

Bioimage informatics: a new area of engineering biology.
Peng H., Bioinformatics 24(17), 2008
PMID: 18603566
Bioimage informatics for experimental biology.
Swedlow JR, Goldberg IG, Eliceiri KW; OME Consortium., Annu Rev Biophys 38(), 2009
PMID: 19416072
Open source bioimage informatics for cell biology.
Swedlow JR, Eliceiri KW., Trends Cell Biol. 19(11), 2009
PMID: 19833518
Imaging in systems biology.
Megason SG, Fraser SE., Cell 130(5), 2007
PMID: 17803903
The potential of high-content high-throughput microscopy in drug discovery.
Starkuviene V, Pepperkok R., Br. J. Pharmacol. 152(1), 2007
PMID: 17603554
Quantitative microscopy and systems biology: seeing the whole picture.
Verveer PJ, Bastiaens PI., Histochem. Cell Biol. 130(5), 2008
PMID: 18830616
MALDI imaging mass spectrometry: molecular snapshots of biochemical systems.
Cornett DS, Reyzer ML, Chaurand P, Caprioli RM., Nat. Methods 4(10), 2007
PMID: 17901873
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
Multi-modal imaging of histological tissue sections.
Can A, Bello M, Cline H, Tao X, Ginty F., 2008
Multiplexed analysis of proteins in tissue using multispectral fluorescence imaging.
Barash E, Dinn S, Sevinsky C, Ginty F., IEEE Trans Med Imaging 29(8), 2010
PMID: 20304722
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
Toponome Imaging System (TIS): imaging the proteome with functional resolution.
Bode M, Krusche A., 2007
Integrating semantic annotation and information visualization for the analysis of multichannel fluorescence micrographs from pancreatic tissue.
Herold J, Zhou L, Abouna S, Pelengaris S, Epstein D, Khan M, Nattkemper TW., Comput Med Imaging Graph 34(6), 2009
PMID: 19969439
Multivariate image mining.
Herold J, Loyek C, Nattkemper TW., 2011
Towards protein network analysis using TIS imaging and exploratory data analysis.
Langenkämper D, Kölling J, Humayun A, Abouna S, Epstein D., 2011
Image registration methods: a survey.
Zitova B., 2003
Mutual-information-based registration of medical images: a survey.
Pluim JP, Maintz JB, Viergever MA., IEEE Trans Med Imaging 22(8), 2003
PMID: 12906253
A survey of medical image registration.
Maintz JB, Viergever MA., Med Image Anal 2(1), 1998
PMID: 10638851
A review of recent range image registration methods with accuracy evaluation.
Salvi J, Matabosch C, Fofi D, Forest J., 2007
Multi-modal volume registration by maximization of mutual information.
Wells WM 3rd, Viola P, Atsumi H, Nakajima S, Kikinis R., Med Image Anal 1(1), 1996
PMID: 9873920
Multimodality image registration by maximization of mutual information.
Maes F, Collignon A, Vandermeulen D, Marchal G, Suetens P., IEEE Trans Med Imaging 16(2), 1997
PMID: 9101328
Mutual information-based multimodal image registration using a novel joint histogram estimation.
Lu X, Zhang S, Su H, Chen Y., Comput Med Imaging Graph 32(3), 2008
PMID: 18215504
A Comprehensive Approach for Multi-channel Image Registration.
Rohde GK, Pajevic S, Pierpaoli C, Basser PJ., 2003
Multi-channel registration of diffusion tensor images using directional information.
Rohde GK, Pajevic S, Pierpaoli C., 2004
Multichannel image registration by feature-based information fusion.
Li Y, Verma R., IEEE Trans Med Imaging 30(3), 2010
PMID: 21097379
Alignment of the cell nucleus from labeled proteins only for 4D in vivo imaging.
Rieger B, Molenaar C, Dirks RW, Van Vliet LJ., Microsc. Res. Tech. 64(2), 2004
PMID: 15352085
A correlation-based approach to calculate rotation and translation of moving cells.
Wilson CA, Theriot JA., IEEE Trans Image Process 15(7), 2006
PMID: 16830914
Fast point-based 3-D alignment of live cells.
Matula P, Matula P, Kozubek M, Dvorak V., IEEE Trans Image Process 15(8), 2006
PMID: 16900692
M-FISH image registration and classification.
Wang YP., 2004
Non-rigid temporal registration of 2d and 3d multi-channel microscopy image sequences of human cells.
Kim I, Yang S, Baccon P, Heard E, Chen YC., 2007

Gonzalez RC, Woods RE., 2008
Putting proteins on the map.
Murphy RF., Nat. Biotechnol. 24(10), 2006
PMID: 17033657
Identification of colon cancer specific protein clusters by toponome imaging system and their cellular annotation by using a three symbol code.
Bhattacharya S., 2011
Nonrigid registration of 3-d multichannel microscopy images of cell nuclei.
Yang S, Kohler D, Teller K, Cremer T, Le Baccon P, Heard E, Eils R, Rohr K., IEEE Trans Image Process 17(4), 2008
PMID: 18390358
A hierarchical approach to elastic registration based on mutual information.
Likar B., 2001
Analysis of Generalized Pattern Searches.
Audet C, Dennis JE., 2002
A generating set direct search augmented Lagrangian algorithm for optimization with a combination of general and linear constraints.
Kolda TG, Lewis RM, Torczon V., 2006
Cubic convolution interpolation for digital image processing.
Keys RG., 1981

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 22363510
PubMed | Europe PMC

Suchen in

Google Scholar