Implementing image analysis in laboratory-based experimental systems for ecology and evolution: A hands-on guide

Methods in Ecology and Evolution

Volumn 4, Issue 5, 2013, Pages 483-492

  Pennekamp, Frank ^a   Schtickzelle, Nicolas ^a  

^a EARTH AND LIFE INSTITUTE   (Belgium)

Author keywords

Experimental ecology; ImageJ; Mesocosm; Microbial ecology; Microcosm; Python; R; Technology; Tetrahymena thermophila

Indexed keywords

EID: 84877910050     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/2041-210X.12036     Document Type: Article

References (50)

1. Asai, D.J. & Forney, J.D. (1999) Tetrahymena Thermophila. Methods in Cell Biology, Volume 62. Academic Press, San Diego.
2. Benhaïm, D., Péan, S., Lucas, G., Blanc, N., Chatain, B. & Bégout, M.-L. (2012) Early life behavioural differences in wild caught and domesticated sea bass (Dicentrarchus labrax). Applied Animal Behaviour Science, 141, 79-90.
3. Benton, T.G., Solan, M., Travis, J.M.J. & Sait, S.M. (2007) Microcosm experiments can inform global ecological problems. Trends in Ecology & Evolution, 22, 516-521.
4. Berg, M.P., Kiers, E., Driessen, G., Van Der Heijden, M., Kooi, B.W., Kuenen, F., Liefting, M., Verhoef, H.A. & Ellers, J. (2010) Adapt or disperse: understanding species persistence in a changing world. Global Change Biology, 16, 587-598.
5. Beveridge, O.S., Petchey, O.L. & Humphries, S. (2010) Direct and indirect effects of temperature on the population dynamics and ecosystem functioning of aquatic microbial ecosystems. Journal of Animal Ecology, 79, 1324-1331.
6. Bolnick, D.I., Svanbäck, R., Fordyce, J.A., Yang, L.H., Davis, J.M., Hulsey, C.D. & Forister, M.L. (2003) The ecology of individuals: incidence and implications of individual specialization. The American Naturalist, 161, 1-28.
7. Bolnick, D.I., Amarasekare, P., Araújo, M.S., Bürger, R., Levine, J.M., Novak, M., Rudolf, V.H.W., Schreiber, S.J., Urban, M.C. & Vasseur, D.A. (2011) Why intraspecific trait variation matters in community ecology. Trends in Ecology & Evolution, 26, 183-192.
8. Bowler, D.E. & Benton, T.G. (2010) Testing the interaction between environmental variation and dispersal strategy on population dynamics using a soil mite experimental system. Oecologia, 166, 111-119.
9. Brehm-Stecher, B.F. & Johnson, E.A. (2004) Single-cell microbiology: tools, technologies, and applications. Microbiology and Molecular Biology Reviews, 68, 538-559.
10. Burger, W. & Burge, M. (2008) Digital Image Processing: An Algorithmic Introduction Using Java. Springer, New York.
11. Chaine, A.S., Schtickzelle, N., Polard, T., Huet, M. & Clobert, J. (2010) Kin-based recognition and social aggregation in a ciliate. Evolution, 64, 1290-1300.
12. Correll, N., Sempo, G., Lopez de Meneses, Y., Halloy, J., Deneubourg, J.-L. & Martinoli, A. (2006) SwisTrack: a Tracking Tool for Multi-Unit Robotic and Biological Systems. 2006 IEEE/RSJ International Conference on Intelligent Robots and Systems 9-15 October 2006, Beijing, China pp. 2185-2191.
13. Culverhouse, P.F., Williams, R., Benfield, M., Flood, P.R., Sell, A.F., Mazzocchi, M.G., Buttino, I. & Sieracki, M. (2006) Automatic image analysis of plankton: future perspectives. Marine Ecology Progress Series, 312, 297-309.
14. Daims, H. & Wagner, M. (2007) Quantification of uncultured microorganisms by fluorescence microscopy and digital image analysis. Applied Microbiology and Biotechnology, 75, 237-248.
15. DeLong, J.P. & Hanson, D.T. (2011) Warming alters density dependence, energetic fluxes, and population size in a model algae. Ecological Complexity, 8, 320-325.
16. Drake, J.M. & Griffen, B.D. (2009) Speed of expansion and extinction in experimental populations. Ecology Letters, 12, 772-778.
17. Færøvig, P.J., Andersen, T. & Hessen, D.O. (2002) Image analysis of Daphnia populations: non-destructive determination of demography and biomass in cultures. Freshwater Biology, 47, 1956-1962.
18. Fjerdingstad, E.J., Schtickzelle, N., Manhes, P., Gutierrez, A. & Clobert, J. (2007) Evolution of dispersal and life history strategies - Tetrahymena ciliates. BMC Evolutionary Biology, 7:133
19. Fraser, L.H. & Keddy, P. (1997) The role of experimental microcosms in ecological research. Trends in Ecology & Evolution, 12, 478-481.
20. Fussmann, G.F., Ellner, S.P., Hairston, J., Jones, L.E., Shertzer, K.W. & Yoshida, T. (2005) Ecological and Evolutionary Dynamics of Experimental Plankton Communities. Population Dynamics and Laboratory Ecology (ed R.A. Desharnais), pp. 221-243. Academic Press, London.
21. Gonzalez, R.C. & Woods, R.E. (2002) Digital Image Processing, 2nd edn. Prentice Hall.
22. Gorsky, G., Ohman, M.D., Picheral, M., Gasparini, S., Stemmann, L., Romagnan, J.B., Cawood, A., Pesant, S., García-Comas, C. & Prejger, F. (2010) Digital zooplankton image analysis using the ZooScan integrated system. Journal of Plankton Research, 32, 285-303.
23. Grant, B.R. & Grant, P.R. (1993) Evolution of Darwin's finches caused by a rare climatic event. Proceedings of the Royal Society of London, Biological Sciences, 251, 111-117.
24. Haddad, N.M., Holyoak, M., Mata, T.M., Davies, K.F., Melbourne, B.A. & Preston, K. (2008) Species' traits predict the effects of disturbance and productivity on diversity. Ecology Letters, 11, 348-356.
25. Haddock, S. & Dunn, C. (2010) Practical Computing for Biologists. Sinauer Associates, Sunderland.
26. Hairston, N.G., Ellner, S.P., Geber, M.A., Yoshida, T. & Fox, J.A. (2005) Rapid evolution and the convergence of ecological and evolutionary time. Ecology Letters, 8, 1114-1127.
27. Holyoak, M. & Lawler, S.P. (2005) The contribution of laboratory experiments on protists to understanding population and metapopulation dynamics. Population Dynamics and Laboratory Ecology (ed R.A. Desharnais), pp. 245-266. Academic Press, London.
28. Hooper, H.L., Connon, R., Callaghan, A., Maund, S.J., Liess, M., Duquesne, S., Hutchinson, T.H., Moggs, J. & Sibly, R.M. (2006) The use of image analysis to estimate population growth rate in Daphnia magna. Journal of Applied Ecology, 43, 828-834.
29. Jessup, C.M., Kassen, R., Forde, S.E., Kerr, B., Buckling, A., Rainey, P.B. & Bohannan, B.J.M. (2004) Big questions, small worlds: microbial model systems in ecology. Trends in Ecology & Evolution, 19, 189-197.
30. Kirk, K.L. (1997) Life-History responses to variable environments: starvation and reproduction in planktonic rotifers. Ecology, 78, 434-441.
31. Kirk, K.L. (1998) Enrichment can stabilize population dynamics: autotoxins and density dependence. Ecology, 79, 2456-2462.
32. Laakso, J., Loytynoja, K. & Kaitala, V. (2003) Environmental noise and population dynamics of the ciliated protozoa Tetrahymena thermophila in aquatic microcosms. Oikos, 102, 663-671.
33. Lukas, J., Kucerova, Z. & Stejskal, V. (2009) Computer-based image analysis to quantify the number of micro-arthropods in a sample. Entomologia Experimentalis et Applicata, 132, 289-294.
34. Mallard, F., Le Bourlot, V. & Tully, T. (2012) Automatic particle analysis as sensors for life history studies in experimental microcosms. Sensors for Ecology (eds J.-F. Le Gaillard, J.-M. Guarini & F. Gaill), pp. 163-184. CNRS, Paris.
35. Marçal, A. & Caridade, C. (2006) A System for Automatic Counting the Number of Collembola Individuals on Petri Disk Images. Image Analysis and Recognition Lecture Notes in Computer Science (eds A. Campilho & M. Kamel), pp. 814-822. Springer, Berlin/Heidelberg.
36. Matthiessen, B. & Hillebrand, H. (2006) Dispersal frequency affects local biomass production by controlling local diversity. Ecology Letters, 9, 652-662.
37. Ozgul, A., Coulson, T., Reynolds, A., Cameron, T.C. & Benton, T.G. (2012) Population responses to perturbations: the importance of trait-based analysis illustrated through a microcosm experiment. The American Naturalist, 179, 582-594.
38. Pau, G., Oles, A., Dodd, M. & Sklyar, O. & Huber, W. (2012) EBImage: Image Processing Toolbox for R. Available at: http://www.bioconductor.org/packages/2.12/bioc/html/EBImage.html (accessed 20/2/2013)
39. Pedersen, J.S. (2008) C. elegans motility analysis in ImageJ - A practical approach. http://www.phage.dk/plugins/wrmtrck.html[accessed 25 October 2012].
40. R Development Core Team (2012) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
41. Rodenacker, K., Hense, B., Jütting, U. & Gais, P. (2006) Automatic analysis of aqueous specimens for phytoplankton structure recognition and population estimation. Microscopy Research and Technique, 69, 708-720.
42. Roerdink, J.B.T.M. & Meijster, A. (2000) The watershed transform: definitions, algorithms and parallelization strategies. Fundamenta Informaticae, 41, 187-228.
43. Schillinger, C., Petrich, A., Lux, R., Riep, B., Kikhney, J., Friedmann, A., Wolinsky, L.E., Göbel, U.B., Daims, H. & Moter, A. (2012) Co-localized or randomly distributed? Pair cross correlation of in vivo grown subgingival biofilm bacteria quantified by digital image analysis. PLoS ONE, 7, e37583.
44. Schneider, C.A., Rasband, W.S. & Eliceiri, K.W. (2012) NIH Image to ImageJ: 25 years of image analysis. Nature Methods, 9, 671-675.
45. Schtickzelle, N., Fjerdingstad, E., Chaine, A. & Clobert, J. (2009) Cooperative social clusters are not destroyed by dispersal in a ciliate. BMC Evolutionary Biology, 9, 251.
46. Tully, T. & Ferrière, R. (2008) Reproductive flexibility: genetic variation, genetic costs and long-term evolution in a collembola. PLoS ONE, 3, e3207.
47. Vasseur, D.A. & Fox, J.W. (2009) Phase-locking and environmental fluctuations generate synchrony in a predator-prey community. Nature, 460, 1007-1010.
48. Weeks, P.J.D. & Gaston, K.J. (1997) Image analysis, neural networks, and the taxonomic impediment to biodiversity studies. Biodiversity and Conservation, 6, 263-274.
49. Wiegand, T. & Moloney, A. (2004) Rings, circles, and null-models for point pattern analysis in ecology. Oikos, 104, 209-229.
50. Yoshida, T., Jones, L.E., Ellner, S.P., Fussmann, G.F. & Hairston, N.G. (2003) Rapid evolution drives ecological dynamics in a predator-prey system. Nature, 424, 303-306.