Labour-efficient in vitro lymphocyte population tracking and fate prediction using automation and manual review

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Chakravorty, Rajib ^a   Rawlinson, David ^a   Zhang, Alan ^a   Markham, John ^a   Dowling, Mark R ^b,c   Wellard, Cameron ^b,c   Zhou, Jie H S ^b,c   Hodgkin, Philip D ^b,c  

^a UNIVERSITY OF MELBOURNE   (Australia)

^b WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

^c UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATION; CELL CULTURE; CELL DEATH; CELL FATE; CELL GROWTH; CELL LINEAGE; CELL MOTILITY; CELL SIZE; CELL TRACKING; COMPUTER PROGRAM; CONTROLLED STUDY; HUMAN; HUMAN CELL; HUMAN COMPUTER INTERACTION; IN VITRO STUDY; LYMPHOCYTE SUBPOPULATION; MACHINE LEARNING; PHENOTYPE; PREDICTION; RETROSPECTIVE STUDY; REVIEW; SUPPORT VECTOR MACHINE; TIME-LAPSE VIDEO MICROSCOPY;

CELL TRACKING; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; LYMPHOCYTES; MICROSCOPY, FLUORESCENCE; REPRODUCIBILITY OF RESULTS; SUPPORT VECTOR MACHINES; TIME-LAPSE IMAGING;

EID: 84896802887     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0083251     Document Type: Review

References (54)

1. Schroeder T (2010) The electronic crystal ball: predicting cell fate from timelapse data. Nature Methods 7: 190-191.
2. Collins M (2009) Generating 'omic knowledge': the role of informatics in high content screening. Combinatorial Chemistry & high throughput screening 12.
3. Moller C, Slack M (2010) Impact of new technologies for cellular screening along the drug value chain. Drug Discovery Today 15.
4. Zanella F, Lorens J, Link W (2010) High content screening: seeing is believing. Trends in Biotech-nology 28.
5. Hawkins ED, Markham JF, McGuinness LP, Hodgkin PD (2009) A single-cell pedigree analysis of alternative stochastic lymphocyte fates. Proceedings of the National Academy of Sciences of the United States of America 106: 13457-13462.
6. Meijering E, Dzyubachyk O, Smal I (2012) Methods for cell and particle tracking. Methods in Enzymology 504: 183-200.
7. Bruce V, Henderson Z, Greenwood K, Hancock PJB, Burton AM, et al. (1999) Verification of face identities from images captured on video. Journal of Experimental Psychology: Applied 5.
8. Bruce V, Henderson Z, Newman C, Burton AM (2001) Matching identities of familiar and unfamiliar faces caught on cctv images. Journal of Experimental Psychology: Applied 7: 207-218. (Pubitemid 33595087)
9. Abraham AG, Duncan DD, Gange SJ, West S (2009). Computer-aided assessment of diagnostic images for epidemiological research. BMC Medical Research Methodology. Available: http://www.biomedcentral.com/content/pdf/1471-2288-9-74. pdf. Accessed 2013 Nov 14.
10. Fendley ME (2009) Human cognitive biases and heuristics in image analysis. Ph.D. thesis, Wright State University.
11. Sica G (2006) Bias in research studies. Radiology 238: 780-789. (Pubitemid 43289908)
12. Halin C, Mora J, Sumen C, von Andrian U (2005) In vivo imaging of lymphocyte trafficking. Annual Review of Cell and Developmental Biology 21: 581-603. (Pubitemid 41740647)
13. Witt CM, Raychaudhuri S, Schaefer B, Chakraborty AK, Robey EA (2005) Directed migration of positively selected thymocytes visualized in real time. PLoS Biol 3: e160.
14. Jin T, Xu X, Hereld D (2008) Chemotaxis, chemokine receptors and human disease. Cytokine 44: 1-8.
15. Debeir O, Camby I, Kiss R, Van Ham P, Decaestecker C (2004) A model-based approach for automated in vitro cell tracking and chemotaxis analyses. Cytometry Part A 60A: 29-40. (Pubitemid 38859199)
16. Uppaluri S, Nagler J, Stellamanns E, Heddergott N, Herminghaus S, et al. (2011) Impact of microscopic motility on the swimming behavior of parasites: Straighter trypanosomes are more directional. PLoS Comput Biol 7: e1002058.
17. Higgins JM, Eddington DT, Bhatia SN, Mahadevan L (2009) Statistical dynamics of owing red blood cells by morphological image processing. PLoS Comput Biol 5: e1000288.
18. Instruments K (2011). Manual cell-tracking with fiji. Available: http://www.kairosinstruments.com/wp-content/uploads/2011/07/Manual-Cell- Trackingwith-Fiji.pdf. Accessed: 2010 Sep 30.
19. Rieger MA, Hoppe PS, Smejkal BM, Eitelhuber AC, Schroeder T (2009) Hematopoietic cytokines can instruct lineage choice. Science 325: 217-218.
20. Eilken H, Nishikawa S, Schroeder T (2009) Continuous single-cell imaging of blood generation from haemogenic endothelium. Nature 457: 896-900.
21. Schroeder T (2011) Long-term single-cell imaging of mammalian stem cells. Nature Methods 8.
22. Molecular Devices. Metamorph. Available: http://www.moleculardevices.com/ Products/Software/Meta-Imaging-Series/MetaMorph.html. Accessed 2010 Sep 30.
23. Moogk DR (2009) Live cell imaging, cell tracking and lineage analysis as a tool to investigate dynamic culture processes in heterogeneous cell systems. Ph.D. thesis, Chemical Engineering, Waterloo, Ontario, Canada.
24. Markham J, Wellard C, Hawkins E, Duffy K, Hodgkin P (2010) A minimum of two distinct heritable factors are required to explain correlation structures in proliferating lymphocytes. Journal of the Royal Society, Interface 7: 1049-1059.
25. Zilman A, Ganusov VV, Perelson AS (2010) Stochastic models of lymphocyte proliferation and death. PLoS One 5: e12775.
26. Lamprecht M, Sabatini D, Carpenter A (2007) Cellprofiler: free, versatile software for automated biological image analysis. Biotechniques 42: 71-75.
27. Warwick Systems Biology Centre. Celltracker. Available: http://www2.warwick. ac.uk/fac/sci/systemsbiology/staff/bretschneider/ celltracker/. Accessed 2010 Sep 30.
28. Perkin Elmer. Volocity. Available: http://www.perkinelmer.com/pages/020/ cellularimaging/products/volocity.xhtml. Accessed 2010 Sep 30.
29. Sacan A, Ferhatosmanoglu H, Coskun H (2008) Celltrack: An open-source software for cell tracking and motility analysis. Bioinformatics 24: 1647-1649. (Pubitemid 351966168)
30. Bitplane. Imaris. Available: http://www.bitplane.com/go/products/. Accessed 2010 Sep 30.
31. Warwick Systems Biology Centre. Lineagetracker. Available: http://www2. warwick.ac.uk/fac/sci/systemsbiology/staff/bretschneider/lineagetracker/. Accessed 2010 Sep 30.
32. Downey M, Vance KW, Bretschneider T (2011) Lineagetracker: A statistical scoring method for tracking cell lineages in large cell populations with low temporal resolution. In: IEEE International Symposium on Biomedical Imaging: From Nano to Macro.
33. Li K, Chen M, Kanade T (2007) Cell population tracking and lineage construction with spatiotemporal context. In: 10th International Conference on Medical Image Computing and Computer-Assisted Intervention. pp. 295-302.
34. Bise R, Yin Z, Kanade T (2011) Reliable cell tracking by global data association. IEEE International Symposium on Biomedical Imaging.
35. Brown MR, Summers HD, Rees P, Smith PJ, Chappell SC, et al. (2010) Flowbased cytometric analysis of cell cycle via simulated cell populations. PLoS Comput Biol 6: e1000741.
36. Julius MH, Masuda T, Herzenberg LA (1972) Demonstration that antigenbinding cells are precursors of antibody-producing cells after purification with a uorescence-activated cell sorter. Proceedings of the National Academy of Sciences of the United States of America 69: 1934-1938.
37. Duffy KR, Wellard CJ, Markham JF, Zhou JHS, Holmberg R, et al. (2012) Activation-induced b cell fates are selected by intracellular stochastic competition. Science 335: 338-341.
38. Rapoport D, Becker T, Mamlouk AM, Schicktanz S, Kruse C (2011) A novel validation algorithm allows for automated cell tracking and the extraction of biologically meaningful parameters. PLoS ONE 6.
39. Scherf N, Franke K, Glauche I, Kurth I, Bornhuser M, et al. (2012) On the symmetry of siblings: automated single-cell tracking to quantify the behavior of hematopoietic stem cells in a biomimetic setup. Experimental Hematology 40: 119-130.
40. Rasband W (1997-2012). Imagej. U.S. National Institutes of Health, Bethesda, Maryland, USA. Available: http://imagej.nih.gov/ij. Accessed 2010 Sept 30.
41. Roerdink JB, Meijster A (2001) The watershed transform: Definitions, algorithms and parallelization strategies. Fundamenta Informaticae 41: 187-228.
42. Kachouie N, Fieguth P (2007) Extended-hungarian-jpda: Exact single-frame stem cell tracking. IEEE Trans Biomedical Engineering 54: 2011-2019. (Pubitemid 350010849)
43. Musicki D, Evans R (2002) Linear joint integrated probabilistic data association-ljipda. In: Proc. 41st IEEE Conference on Decision and Control. volume 3, pp. 2415-2420.
44. Cohen A, Gomes F, Roysam B, Cayouette M (2010) Computational prediction of neural progenitor cell fates. Nature methods 7: 213-218.
45. Al-Kofahi O, Radke R, Goderie S, Qin S, Temple S, et al. (2006) Automated cell lineage construction: a rapid method to analyze clonal development established with murine neural progenitor cells. Cell Cycle 5: 327-335. (Pubitemid 43213505)
46. Hawkins E, Hommel M, Turner M, Battye F, Markham J, et al. (2007) Measuring lymphocyte proliferation, survival and differentiation using cfse timeseries data. Nature Protocols 2: 2057-2067. (Pubitemid 351565843)
47. Zhou J, Bischof WF, Caelli T (2006) Road tracking in aerial images based on human-computer interaction and bayesian filtering. ISPRS Journal of Photogrammetry and Remote Sensing 61: 108-124. (Pubitemid 46053758)
48. Zhou J, Cheng L, Caelli T, Bischof WF (2007) Knowledge transfer in semiautomatic image interpretation. In: 12th international conference on Humancomputer interaction: intelligent multimodal interaction environments. pp. 1028-1034.
49. Pavlidis T (1978) A minimum storage boundary tracing algorithm and its application in automatic inspection. IEEE Transactions on Systems, Man and Cybernetics 8: 66-69. (Pubitemid 8572577)
50. Challa S, Evans R, Musicki D (2002) Target tracking-a bayesian perspective. volume 1, pp. 437-440.
51. Bar-Shalom Y (1975) Tracking in a cluttered environment with probabilistic data association. Automatica 11: 451-460.
52. Fortmann T, Bar-Shalom Y, Scheffe M (1980) Multi-target tracking using joint probabilistic data association. In: Proc. of 19th IEEE Conference on Decision and Control. volume 19, pp. 807-812. (Pubitemid 11475718)
53. Musicki D, Evans R, Stankovic S (1994) Integrated probabilistic data association. IEEE Trans Automatic Control 39: 1237-1241.
54. Kan A, Chakravorty R, Bailey J, Leckie C, Markham J, et al. (2011) Automated and semi-automated cell tracking: Addressing portability challenges. Journal of Microscopy 244: 194-213.