RAMTaB: Robust Alignment of Multi-Tag Bioimages
Raza S-E-A, Epstein D, Nattkemper TW, Rajpoot N (2012)
PLoS ONE 7(2): e30894.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
Download
Autor*in
Raza, Shan-E-Ahmed;
Epstein, David;
Nattkemper, Tim WilhelmUniBi ;
Rajpoot, Nasir
Einrichtung
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.
Stichworte
bioimage informatics;
image registration;
MELC;
toponomics;
TIS
Erscheinungsjahr
2012
Zeitschriftentitel
PLoS ONE
Band
7
Ausgabe
2
Art.-Nr.
e30894
ISSN
1932-6203
eISSN
1932-6203
Page URI
https://pub.uni-bielefeld.de/record/2455753
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, Shan-E-Ahmed, Epstein, David, Nattkemper, Tim Wilhelm, and Rajpoot, Nasir. 2012. “RAMTaB: Robust Alignment of Multi-Tag Bioimages”. PLoS ONE 7 (2): e30894.
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): e30894.
S.-E.-A. Raza, et al., “RAMTaB: Robust Alignment of Multi-Tag Bioimages”, PLoS ONE, vol. 7, 2012, : 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:
Dieses Objekt ist durch das Urheberrecht und/oder verwandte Schutzrechte geschützt. [...]
Volltext(e)
Access Level
Open Access
Zuletzt Hochgeladen
2019-09-06T09:17:58Z
MD5 Prüfsumme
cc6ec8f91e12d4e5497f358226ee6364
Link(s) zu Volltext(en)
Access Level
Closed Access
Daten bereitgestellt von European Bioinformatics Institute (EBI)
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
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
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
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
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
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
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
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
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
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
Swedlow JR, Eliceiri KW., Trends Cell Biol. 19(11), 2009
PMID: 19833518
The potential of high-content high-throughput microscopy in drug discovery.
Starkuviene V, Pepperkok R., Br. J. Pharmacol. 152(1), 2007
PMID: 17603554
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
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
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
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
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
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
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
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
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
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
Langenkämper D, Kölling J, Humayun A, Abouna S, Epstein D., 2011
Image registration methods: a survey.
Zitova B., 2003
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
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
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
Salvi J, Matabosch C, Fofi D, Forest J., 2007
Mutual information-based CT-MR brain image registration using generalized partial volume joint histogram estimation.
Chen HM, Varshney PK., IEEE Trans Med Imaging 22(9), 2003
PMID: 12956266
Chen HM, Varshney PK., IEEE Trans Med Imaging 22(9), 2003
PMID: 12956266
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
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
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
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
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
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
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
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
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
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
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
Kim I, Yang S, Baccon P, Heard E, Chen YC., 2007
Image matching as a diffusion process: an analogy with Maxwell's demons.
Thirion JP., Med Image Anal 2(3), 1998
PMID: 9873902
Thirion JP., Med Image Anal 2(3), 1998
PMID: 9873902
Gonzalez RC, Woods RE., 2008
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, Mathew G, Ruban E, Epstein DB, Krusche A, Hillert R, Schubert W, Khan M., J. Proteome Res. 9(12), 2010
PMID: 20822185
Bhattacharya S, Mathew G, Ruban E, Epstein DB, Krusche A, Hillert R, Schubert W, Khan M., J. Proteome Res. 9(12), 2010
PMID: 20822185
Fluorescence detection of protein clusters in individual cells and tissue sections by using toponome imaging system: sample preparation and measuring procedures.
Friedenberger M, Bode M, Krusche A, Schubert W., Nat Protoc 2(9), 2007
PMID: 17853885
Friedenberger M, Bode M, Krusche A, Schubert W., Nat Protoc 2(9), 2007
PMID: 17853885
Toponome 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.
Schubert W, Gieseler A, Krusche A, Hillert R., J. Proteome Res. 8(6), 2009
PMID: 19275201
Schubert W, Gieseler A, Krusche A, Hillert R., J. Proteome Res. 8(6), 2009
PMID: 19275201
Identification of colon cancer specific protein clusters by toponome imaging system and their cellular annotation by using a three symbol code.
Bhattacharya S., 2011
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
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
Likar B., 2001
Analysis of Generalized Pattern Searches.
Audet C, Dennis JE., 2002
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
Kolda TG, Lewis RM, Torczon V., 2006
Cubic convolution interpolation for digital image processing.
Keys RG., 1981
Keys RG., 1981
Export
Markieren/ Markierung löschen
Markierte Publikationen
Web of Science
Dieser Datensatz im Web of Science®Quellen
PMID: 22363510
PubMed | Europe PMC
Suchen in