Single-cell-based image analysis of High-throughput cell array screens for quantification of viral infection

Cytometry Part A

Volumn 75, Issue 4, 2009, Pages 309-318

  Matula, Petr ^a,b,c   Kumar, Anil ^a   Wörz, Ilka ^a   Erfle, Holger ^a   Bartenschlager, Ralf ^a   Eils, Roland ^a,b   Rohr, Karl ^a,b  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^c MASARYK UNIVERSITY   (Czech Republic)

Author keywords

Cell nucleus segmentation; Cell based arrays; Image analysis; Image quality control; Immunofluorescence microscopy; Quantification of viral infection; Sirna screening

Indexed keywords

SMALL INTERFERING RNA;

ARTICLE; CELL NUCLEUS; FLUORESCENCE MICROSCOPY; HIGH THROUGHPUT SCREENING; IMAGE ANALYSIS; IMAGE QUALITY; PRIORITY JOURNAL; QUALITY CONTROL; VIRUS INFECTION;

ALGORITHMS; CELL NUCLEUS; CELL SHAPE; DENGUE; DNA, VIRAL; HEPATITIS C; HUMANS; IMAGE CYTOMETRY; MICROSCOPY, FLUORESCENCE; PREDICTIVE VALUE OF TESTS; RNA INTERFERENCE; RNA, SMALL INTERFERING; TIME FACTORS; TISSUE ARRAY ANALYSIS; VIRUS DISEASES;

EID: 65549144451     PISSN: 15524922     EISSN: 15524930     Source Type: Journal    
DOI: 10.1002/cyto.a.20662     Document Type: Article

References (34)

1. Damm E, Pelkmans L. Systems biology of virus entry in mammalian cells. Cell Microbiol 2006;8:1219-1227.
2. Carpenter AE, Sabatini DM, Systernalic genome-wide screens of gene function, Nat Rev Genet 2004;5:11-22.
3. Pelkmans L, Fava E3 Grabner H, Hannas M, Haberrnann B, Krausz E3 Zerial M. Genome-wide analysis of human kinases in clathrin- and caveolac/raft-mediated endocytosis. Nature 2005;436:78-86.
4. Erfle H, Simpson |C, Bastiaens PIH, Pcppcrkok R, siRNA tell arrays for high-content screening microscopy. Biotechniques 2004;37:454-462.
5. Perrimon N, Matbey-Prevot B. Applications of high-throughput RNA interference screens to problems in cell and developmental biology. Genetics 2007; 175:7-16.
6. Echeverri Cj, Perrimon N, High-throughput RNAI screening in cultured cells: A user's guide. Nat Rev Genet 2006;7:373-384.
7. Elter M, Daum V, Wittenberg T. Maximum-intensity-linking for segmentation of fluorescence-stained cells. In: Metaxas D, Whitaker K3 Rittscher), Sebastian T, editors. Proceedings of MICCAI, Workshop MIAAB, Copenhagen: Fraunhofcr Publica; 2006. pp 46-50.
8. Lin G, Ghawla MK, Olson K, Guzowski IF, Barnes CA, Roysam B. Hierarchical model-based merging of multiple fragments for improved three-dimensional segmentation of nuclei. Cytometry Part a"2005;63A:20-33.
9. Lindblad J. Wählhy C, Bengtsson E, Zaltsman A. Image analysis for automatic seg-meniation of cytoplasm and classification of Racl activation, Cytometry Part A 20G4;27A:22-33
10. Wablby C, Lindblad J, Yondrus M, Bengtsson K, Björkesten L, Algorithms for cytoplasm segmentation of fluorescence labelled cells. Anal Cell Pathol 2002;24:101-111.
11. Adiga PSU, Chaudhuri BB. An efficient method based on watershed and rule-based merging for segmentation of 3-D histo-palhological images. Pattern Recognit 2001;34:1449-1458.
12. Li F, Zhou X, Ma L. Wong STC. An automated feedback system with the hybrid model of scoring and classification for solving over-segmentation problems in RNAi high-content screening. JMicrosc2007;226:121-132.
13. Harder N, Mora-Benmidez F, Godinez WJ, Ellen berg j, Hils R, Rohr K. Automated analysis of the mitotic phases of human cells in 5D fluorescence microscopy image sequences. In; Larsen R, Nielsen M, Sponing j, editors. Proceedings of MICCAI'06, LNCS 4190. Copenhagen: Springer-Verlag; 2006. pp 840-848.
14. Yang X, Li H, Zhou X. Nuclei segmentation using marker-controlled watershed; tracking using mean-shift, and Kalnian filter in time-lapse microscopy. IEEE Trans Circuits Syst I 2006;53:2405-2414.
15. 3 Guertin DAj ("hang JH, Lindquist RA, Moffat J, CkJlland P, Sabatini DM. Cell Profiler: Image analysis software for identifying and quantifying cell phenotypes. Genome Biol 2006;7: R100.
16. Raman S, Maxwell CA, Barcellos-Hoff MH, Parvin B. Geometric approach to segmentation and protein localization in cell cultures assays. J Microsc 2007;225:22-30.
17. Gudla PR, Nandy K, Collins J, Meaburn KJ, Misteli T, Locked SJ. A high-throughput system for segmenting nuclei using multiscale techniques. Cylomelry Part A 2008;73A:451-466.
18. Perlman ZK, Slack MD, Feng Y, Milchison Tj, Wu LF Altschuler Sj. Multidimensional drug profiling by automated microscopy. Science 2004;306:1194-1198.
19. Xiong GLj Zhou XB, Ji L, Automated segmentation of Drosophila RNAi fluorescence cellular images using deformable models. IKFE Trans Circuits Syst 1 2006;53;2415-2424.
20. Jones TRj Carpenter A, Gotland P. Voronoi-based segmentation of cells on image manifolds. In: Liu Y, Juany T, Zhang C, editors. Proceedings of Computer Vision for Biomedical Image Applications Conference. LNCS 3765. Berlin, Heidelberg: Springer-Verlag; 2005. pp 535-543.
21. Chang H, Yang Q, Parvin B. Segmentation of heterogenous blob objects through voting and level set formulation. Pattern Recognit Lett 2007;28:1781-1787.
22. Gonzalez RC, Woods RE. Digital Image Processing. Prentice Hall. New Jersey, USA; 2002.
23. DIPImage Toolbox. Available at: Http://www.diplib.org/.
24. Soille P. Morphological Image Analysis: Principles and Applications, 2nd ed. Berlin, Germany: Springer; 2004.
25. Zhang JH, Chung TD, Oldenburg KR. A simple statistical parameter for use in evaluation and validation of high throughput screening assays, j Biomol Screen 1999; 4:67-73.
26. Nakabayashi H, Takela K, Miyano K, Yamane T, Sato J. Growth of human hepatoma cell lines with differentiated functions in chemically defined medium. Cancer Res 1982;42:3858-3863.
27. Blight Kjj McKeating JA, Rice CM. Highly permissive cell lines for subgenomic and genomic hepatitis C virus RNA replication. I Virol 2002;76:J300J-13014.
28. Schaller T, Appel N, Koutsoudakis G, Kallis Sj Lohmann Vj Pietschmann T, Ban ens-chlager R. Analysis of hepatitis C virus superinfecfion exclusion by using novel fiuor-ochrome gene-tagged viral genomes, j Virol 2007 1:4591-4603.
29. Otsu N. A threshold selection method from gray level histograms. IEEE Trans Syst ManCybern 1979;9:62-66.
30. CellProfiler. Available at: Http://www.cellprofiler.org/.
31. Sun Y, Duthaler S, Nelson BJ. Autofocusing in computer microscopy: Selecting the optimal focus algorithm. Microsc Res Tech 2004:65:139-149.
32. Levsky JM, Singer RH. Gene expression and the myth of the average cell. Trends Cell Biol 2003:13:4-6.
33. Firestone L, Cook K, Gulp K, Talsania N, Preston K jr. Comparison of autofocus methods for automated microscopy. Cy tome try 1991;12:195-206.
34. Groen FCA, Young IT, Ligthart G. A comparison of different focus functions for use in autofocus algorithms. Cytometry 1985;6:81-91.