An active-contour based algorithm for the automated segmentation of dense yeast populations on transmission microscopy images

Computing and Visualization in Science

Volumn 14, Issue 7, 2011, Pages 341-352

  Bredies, Kristian ^a   Wolinski, Heimo ^a  

^a UNIVERSITY OF GRAZ   (Austria)

Author keywords

Active contour algorithm; Cell segmentation; Dense yeast populations; Transmission microscopy

Indexed keywords

CELLS; CYTOLOGY; POPULATION STATISTICS; YEAST;

ACTIVE CONTOUR ALGORITHMS; AUTOMATED SEGMENTATION; CELL SEGMENTATION; DENSE YEAST POPULATIONS; HETEROGENEOUS CHARACTERISTIC; IMAGE PROCESSING PIPELINE; NON-INVASIVE DETECTION; TRANSMISSION MICROSCOPY;

IMAGE SEGMENTATION;

EID: 84871798868     PISSN: 14329360     EISSN: 14330369     Source Type: Journal    
DOI: 10.1007/s00791-012-0178-8     Document Type: Article

References (24)

1. Bredies, K.: A variational weak weighted derivative: Sobolev spaces and degenerate elliptic equations. Tech. rep., University of Bremen (2008)
2. Buades, A., Coll, B., Morel, J.M.: A review of image denoising algorithms, with a new one. Multiscale Model. Simul. 4(2), 490- 530 (2005)
3. Carpenter, A.E., Jones, T.R., Lamprecht, M.R., Clarke, C., Kang, I.H., Friman, O., Guertin, D.A., Chang, J.H., Lindquist, R.A., Moffat, J., Golland, P., Sabatini, D.M.: Cellprofiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 7(10), R100 (2006)
4. Caselles, V., Catté, F., Coll, T., Dibos, F.: A geometric model for active contours in image processing. Numerische Mathematik 66(1), 1-31 (1993)
5. Caselles, V., Kimmel, R., Sapiro, G.: Geodesic active contours. Int. J. Comput. Vis. 22(1), 61-79 (1997)
6. Catté, F., Lions, P.L., Morel, J.M., Coll, T.: Image selective smoothing and edge detection by nonlinear diffusion. SIAM J. Numer. Anal. 29(1), 182-193 (1992)
7. Chan, T.F., Shen, J.: Image Processing and Analysis - Variational, PDE, Wavelet, and Stochastic Methods. SIAM, Philadelphia (2005)
8. Hamilton, N.A., Pantelic, R.S., Hanson, K., Teasdale, R.D.: Fast automated cell phenotype image classification. BMC Bioinf. 8, 110 (2007)
9. Huh, S., Lee, D., Murphy, R.F.: Efficient framework for automated classification of subcellular patterns in budding yeast. Cytom. A 75(11), 934-940 (2009)
10. Huh, W.K., Falvo, J.V., Gerke, L.C., Carroll, A.S., Howson, R.W., Weissman, J.S., O'Shea, E.K.: Global analysis of protein localization in budding yeast. Nature 425(6959), 686-691 (2003)
11. Kass, M., Witkin, A., Terzopoulos, D.: Snakes: Active Contour Models. Int. J. Comput. Vis. 1(4), 321-331 (1988)
12. Kvarnstrom,M., Logg, K., Diez, A., Bodvard, K., Kall, M.: Image analysis algorithms for cell contour recognition in budding yeast. Opt. Express 16(17), 12943-12957 (2008)
13. Li, Z., Vizeacoumar, F.J., Bahr, S., Li, J., Warringer, J., Vizeacoumar, F.S., Min, R., Vandersluis, B., Bellay, J., Devit, M., Fleming, J.A., Stephens, A., Haase, J., Lin, Z.Y., Baryshnikova, A., Lu, H., Yan, Z., Jin, K., Barker, S., Datti, A., Giaever, G., Nislow, C., Bulawa, C., Myers, C.L., Costanzo, M., Gingras, A.C., Zhang, Z., Blomberg, A., Bloom, K., Andrews, B., Boone, C.: Systematic exploration of essential yeast gene function with temperature-sensitive mutants. Nat. Biotechnol. 29(4), 361-367 (2011)
14. Ohnuki, S., Oka, S., Nogami, S., Ohya, Y.: High-content, image-based screening for drug targets in yeast. PLoS One 5(4), e10177 (2010)
15. Ohya, Y., Sese, J., Yukawa, M., Sano, F., Nakatani, Y., Saito, T.L., Saka, A., Fukuda, T., Ishihara, S., Oka, S., Suzuki, G., Watanabe, M., Hirata, A., Ohtani, M., Sawai, H., Fraysse, N., Latge, J.P., Francois, J.M., Aebi, M., Tanaka, S., Muramatsu, S., Araki, H., Sonoike, K., Nogami, S., Morishita, S.: High-dimensional and large-scale phenotyping of yeast mutants. Proc. Natl. Acad. Sci. USA 102(52), 19015-19020 (2005)
16. Perona, P., Malik, J.: Scale-space and edge detection using anisotropic diffusion. IEEE Trans. Pattern Anal. Mach. Intell. 12(7), 629-639 (1990)
17. Saito, T.L., Ohtani, M., Sawai, H., Sano, F., Saka, A., Watanabe, D., Yukawa,M., Ohya, Y., Morishita, S.: Scmd: saccharomyces cerevisiae morphological database. Nucleic Acids Res. 32(Database issue), D319-D322 (2004)
18. Saito, T.L., Sese, J., Nakatani, Y., Sano, F., Yukawa, M., Ohya, Y., Morishita, S.: Data mining tools for the saccharomyces cerevisiae morphological database. Nucleic Acids Res. 33(Web Server issue), W753-W757 (2005)
19. The MathWorks Inc.: MATLAB, version 7.11.0 (R2010b) (2010)
20. Visage Imaging GmbH: Amira 5.3 Microscopy/ResolveRT (2011)
21. Vizeacoumar, F.J., van Dyk, N., Vizeacoumar, F.S., Cheung, V., Li, J., Sydorskyy, Y., Case, N., Li, Z., Datti, A., Nislow, C., Raught, B., Zhang, Z., Frey, B., Bloom, K., Boone, C., Andrews, B.J.: Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis. J. Cell Biol. 188(1), 69-81 (2010)
22. Weickert, J.: Anisotropic Diffusion in Image Processing. Teubner, Stuttgart (1998)
23. Wolinski, H., Petrovic, U.,Mattiazzi,M., Petschnigg, J., Heise, B., Natter, K., Kohlwein, S.D.: Imaging-based live cell yeast screen identifies novel factors involved in peroxisome assembly. J. Proteome Res. 8(1), 20-27 (2009)
24. Xu, C., Prince, J.L.: Snakes, shapes and gradient vector flow. IEEE Trans. Image Process. 7(3), 359-369 (1998)