Segmentation of virus particle candidates in transmission electron microscopy images

Journal of Microscopy

Volumn 245, Issue 2, 2012, Pages 140-147

  Kylberg, G ^a   Uppstrom M ^b   Hedlund, K O ^c   Borgefors, G ^a   Sintorn, I M ^a  

^a SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

^b VIRONOVA AB   (Sweden)

^c Swedish Institute for Communicable Disease Control   (Sweden)

Author keywords

Radial density profile; Transmission electron microscopy; Virus detection; Virus segmentation

Indexed keywords

HIGH RESOLUTION TRANSMISSION ELECTRON MICROSCOPY; IMAGE SEGMENTATION;

AUTOMATIC SEGMENTATIONS; ELONGATED OBJECTS; LOCAL NEIGHBORHOODS; RADIAL DENSITY PROFILE; REFINEMENT STEP; SEGMENTATION METHODS; TRANSMISSION ELECTRON MICROSCOPY IMAGES; VIRUS DETECTION; VIRUS PARTICLES; VIRUS SEGMENTATION;

VIRUSES;

POLYHEDRIN;

ANIMAL CELL; ARTICLE; NONHUMAN; PRIORITY JOURNAL; STATISTICAL ANALYSIS; TRANSMISSION ELECTRON MICROSCOPY; VIRUS PARTICLE;

EID: 84855787992     PISSN: 00222720     EISSN: 13652818     Source Type: Journal    
DOI: 10.1111/j.1365-2818.2011.03556.x     Document Type: Article

References (25)

1. Bhella, D., Rixon, F.J. & Dargan, D.J. (2000). Cryomicroscopy of human cytomegalovirus virions reveals more densely packed genomic dna than in herpes simplex virus type 1. J. Mol. Biol. 295, 155-161.
2. Biel, S.S. & Madeley, D. (2001). Diagnostic virology-the need for electron microscopy: a discussion paper. J. Clin. Virol. 22, 1-9.
3. Cheng, A., Leung, A., Fellmann, D. et al. (2007). Towards automated screening of two-dimensional crystals. J. Struct. Biol. 160, 324-331.
4. Curry, A., Appleton, H. & Dowsett, B. (2006). Application of transmission electron microscopy to the clinical study of viral and bacterial infections: present and future. Micron 37, 91-106.
5. Gentile, M. & Gelderblom, H.R. (2005). Rapid viral diagnosis: role of electron microscopy. New Microbiol. 28, 1-12.
6. Goldsmith, C.S. & Miller, S.E. (2009). Modern uses of electron microscopy for detection of viruses. Clin. Microbiol. Rev. 22, 552-563.
7. Hazelton, P.R. & Gelderblom, H.R. (2003). Electron microscopy for rapid diagnosis of infectious agents in emergent situations. Emerg. Infect. Dis. 9, 294-303.
8. Kylberg, G., Sintorn, I.-M. & Borgefors, G. (2009a). Towards automated TEM for virus diagnostics: segmentation of grid squares and detection of regions of interest. In Proc. 11th Scandinavian Conference on Image Analysis (ed. by A.-B. Salberg, J.Y. Hardeberg & R. Jenssen ), vol. 5575 of LNCS, pp. 169-178. Springer, Berlin/Heidelberg, Germany.
9. Kylberg, G., Sintorn, I.-M., Uppström, M. & Ryner, M. (2009b) Local intensity and PCA based detection of virus particle candidates in transmission electron microscopy images. In Proceedings of the IEEE 6th International Symposium on Image and Signal Processing and Analysis, University of Salzburg, Salzburg, Austria, pp. 426-431.
10. Lam, L., Lee, S.-W. & Suen, C. (1992). Thinning methodologies - a comprehensive survey. IEEE Trans. Pattern Anal. 14, 869-885.
11. Lefman, J., Morrison, R. & Subramaniam, S. (2007). Automated 100-position specimen loader and image acquisition system for transmission electron microscopy. J. Struct. Biol. 158, 318-326.
12. Madeley, C. (2003). Diagnosing smallpox in possible bioterrorist attack. Lancet 361, 97-98.
13. Matuszewski, B.J. & Shark, L.-K. (2001). Hierarchical iterative bayesian approach to automatic recognition of biological viruses in electron microscope images. In Proceedings of IEEE 2001 International Conference on Image Processing, Thessaloniki, Greece, vol. 2, pp. 347-350.
14. Matuszewski, B.J., Shark, L.-K. & Hall, G. (1997). A novel segmentation and classification method for identification of viruses in electron microscope image. In Proceedings of IEEE 6th International Conference on Image Processing and its Applications, pp. 819-823.
15. Maurer, Jr., C.R., Qi, R. & Raghavan, V. (2003). A linear time algorithm for computing exact Euclidean distance transforms of binary images in arbitrary dimensions. IEEE T. Pattern Anal. 25, 265-270.
16. Meyer, F. & Beucher, S. (1990). Morphological segmentation. J. Vis. Commun. Image R. 1, 21-46.
17. Schramlová, J., Arientová, S. & Hínská, D. (2010). The role of electron microscopy in the rapid diagnosis of viral infections - review. Folia Microbiol. 55, 88-101.
18. Shark, L.-K., Matuszewski, B.J. & Hall, G. (1998). New template matching approach for automatic classification of viruses in electron microscope images. In Proc. of Medical Image Understanding Conference, pp. 157-160. British Machine Vision Association, U.K.
19. Sintorn, I.-M., Homman-Loudiyi, M., Söderberg-Nauclér, C. & Borgefors, G. (2004). A refined circular template matching method for classification of human cytomegalovirus capsids in TEM images. Comput. Meth. Prog. Bio. 76, 95-102.
20. Sonka, M., Hlavac, V. & Boyle, R. (2008). Image Processing, Analysis, and Machine Vision, 3rd edn. Thomson Learning, Toronto, ON, Canada
21. Suloway, C., Pulokas, J., Fellmann, D. et al. (2005). Automated molecular microscopy: the new Leginon system. J. Struct. Biol. 151, 41-60.
22. Utagawa, E.T., Nakazawa, E., Matsuo, K., Oishi, I., Takeda, N. & Miyamura, T. (2002). Application of an automated specimen search system installed in a transmission electron microscope for the detection of caliciviruses in clinical specimens. J. Virol. Methods 100, 49-56.
23. Uttamchandani, M., Neo, J.L., Ong, B.N.Z. & Moochhala, S. (2009). Applications of microarrays in pathogen detection and biodefence. Trends Biotechnol. 27, 53-61.
24. Watts, N.R., Jones, L.N., Cheng, N., Wall, J.S., Parry, D.A.D. & Steven, A.C. (2002). Cryo-electron microscopy of trichocyte (hard α-keratin) intermediate filaments reveals a low-density core. J. Struct. Biol. 137, 109-118.
25. Zhang, J., Nakamura, N., Shimizu, Y. et al. (2009). Jadas: a customizable automated data acquisition system and its application to ice-embedded single particles. J. Struct. Biol. 165, 1-9.