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BEMOVI, software for extracting behavior and morphology from videos, illustrated with analyses of microbes

Bibliographic reference Pennekamp, Frank ; Schtickzelle, Nicolas ; Petchey, Owen L.. BEMOVI, software for extracting behavior and morphology from videos, illustrated with analyses of microbes. In: Ecology and Evolution, Vol. 5, no. 13, p. 2584–2595 (2015)
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  1. Albertsen Mads, Hugenholtz Philip, Skarshewski Adam, Nielsen Kåre L, Tyson Gene W, Nielsen Per H, Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes, 10.1038/nbt.2579
  2. Altermatt Florian, Fronhofer Emanuel A., Garnier Aurélie, Giometto Andrea, Hammes Frederik, Klecka Jan, Legrand Delphine, Mächler Elvira, Massie Thomas M., Pennekamp Frank, Plebani Marco, Pontarp Mikael, Schtickzelle Nicolas, Thuillier Virginie, Petchey Owen L., Big answers from small worlds: a user's guide for protist microcosms as a model system in ecology and evolution, 10.1111/2041-210x.12312
  3. Amaral A. L., Ginoris Y. P., Nicolau A., Coelho M. A. Z., Ferreira E. C., Stalked protozoa identification by image analysis and multivariable statistical techniques, 10.1007/s00216-008-1845-y
  4. Bell Jenefer L., Hopcroft Russell R., Assessment of ZooImage as a tool for the classification of zooplankton, 10.1093/plankt/fbn092
  5. Bolnick Daniel I., Svanbäck Richard, Fordyce James A., Yang Louie H., Davis Jeremy M., Hulsey C. Darrin, Forister Matthew L., The Ecology of Individuals: Incidence and Implications of Individual Specialization, 10.1086/343878
  6. Branson Kristin, Robie Alice A, Bender John, Perona Pietro, Dickinson Michael H, High-throughput ethomics in large groups of Drosophila, 10.1038/nmeth.1328
  7. Brehm-Stecher B. F., Johnson E. A., Single-Cell Microbiology: Tools, Technologies, and Applications, 10.1128/mmbr.68.3.538-559.2004
  8. Breiman Leo, 10.1023/a:1010933404324
  9. Carrara F., Altermatt F., Rodriguez-Iturbe I., Rinaldo A., Dendritic connectivity controls biodiversity patterns in experimental metacommunities, 10.1073/pnas.1119651109
  10. Cutler D. Richard, Edwards Thomas C., Beard Karen H., Cutler Adele, Hess Kyle T., Gibson Jacob, Lawler Joshua J., RANDOM FORESTS FOR CLASSIFICATION IN ECOLOGY, 10.1890/07-0539.1
  11. DeAngelis Donald L., Mooij Wolf M., Individual-Based Modeling of Ecological and Evolutionary Processes, 10.1146/annurev.ecolsys.36.102003.152644
  12. Dell Anthony I., Bender John A., Branson Kristin, Couzin Iain D., de Polavieja Gonzalo G., Noldus Lucas P.J.J., Pérez-Escudero Alfonso, Perona Pietro, Straw Andrew D., Wikelski Martin, Brose Ulrich, Automated image-based tracking and its application in ecology, 10.1016/j.tree.2014.05.004
  13. Elena Santiago F., Lenski Richard E., Microbial genetics: Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation, 10.1038/nrg1088
  14. Schneider Caroline A, Rasband Wayne S, Eliceiri Kevin W, NIH Image to ImageJ: 25 years of image analysis, 10.1038/nmeth.2089
  15. Finlay B. J., Protist taxonomy: an ecological perspective, 10.1098/rstb.2003.1450
  16. Fryxell John M., Lundberg Per, Individual Behavior and Community Dynamics, ISBN:9781489947000, 10.1007/978-1-4899-4698-0
  17. Gaston K. J., O'Neill M. A., Automated species identification: why not?, 10.1098/rstb.2003.1442
  18. Gauze G. F., The struggle for existence, by G. F. Gause., 10.5962/bhl.title.4489
  19. Giometto A., Altermatt F., Carrara F., Maritan A., Rinaldo A., Scaling body size fluctuations, 10.1073/pnas.1301552110
  20. Giometto A., Rinaldo A., Carrara F., Altermatt F., Emerging predictable features of replicated biological invasion fronts, 10.1073/pnas.1321167110
  21. Gorsky G., Ohman M. D., Picheral M., Gasparini S., Stemmann L., Romagnan J.-B., Cawood A., Pesant S., Garcia-Comas C., Prejger F., Digital zooplankton image analysis using the ZooScan integrated system, 10.1093/plankt/fbp124
  22. Holyoak Marcel, Lawler Sharon P., The Contribution of Laboratory Experiments on Protists to Understanding Population and Metapopulation Dynamics, Advances in Ecological Research (2005) ISBN:9780120139378 p.245-271, 10.1016/s0065-2504(04)37008-x
  23. Kawecki Tadeusz J., Lenski Richard E., Ebert Dieter, Hollis Brian, Olivieri Isabelle, Whitlock Michael C., Experimental evolution, 10.1016/j.tree.2012.06.001
  24. Kirchman, Processes in microbial ecology (2012)
  25. Kreft J.-U., Plugge C. M., Grimm V., Prats C., Leveau J. H. J., Banitz T., Baines S., Clark J., Ros A., Klapper I., Topping C. J., Field A. J., Schuler A., Litchman E., Hellweger F. L., Mighty small: Observing and modeling individual microbes becomes big science, 10.1073/pnas.1317472110
  26. Linkert Melissa, Rueden Curtis T., Allan Chris, Burel Jean-Marie, Moore Will, Patterson Andrew, Loranger Brian, Moore Josh, Neves Carlos, MacDonald Donald, Tarkowska Aleksandra, Sticco Caitlin, Hill Emma, Rossner Mike, Eliceiri Kevin W., Swedlow Jason R., Metadata matters: access to image data in the real world, 10.1083/jcb.201004104
  27. Mallard François, Le Bourlot Vincent, Tully Thomas, An Automated Image Analysis System to Measure and Count Organisms in Laboratory Microcosms, 10.1371/journal.pone.0064387
  28. McGill, Evol. Ecol. Res., 8, 691 (2006)
  29. Müller Susann, Nebe-von-Caron Gerhard, Functional single-cell analyses: flow cytometry and cell sorting of microbial populations and communities, 10.1111/j.1574-6976.2010.00214.x
  30. Pennekamp, Swimming with ciliates: dispersal and movement ecology of Tetrahymena thermophila (2014)
  31. Pennekamp Frank, Schtickzelle Nicolas, Implementing image analysis in laboratory-based experimental systems for ecology and evolution: a hands-on guide, 10.1111/2041-210x.12036
  32. Pérez-Escudero Alfonso, Vicente-Page Julián, Hinz Robert C, Arganda Sara, de Polavieja Gonzalo G, idTracker: tracking individuals in a group by automatic identification of unmarked animals, 10.1038/nmeth.2994
  33. Petchey Owen L., Prey diversity, prey composition, and predator population dynamics in experimental microcosms, 10.1046/j.1365-2656.2000.00446.x
  34. R Development Core Team, R: A language and environment for statistical computing (2012)
  35. Roerdink, Fundam. Inform., 41, 187 (2000)
  36. Sbalzarini I.F., Koumoutsakos P., Feature point tracking and trajectory analysis for video imaging in cell biology, 10.1016/j.jsb.2005.06.002
  37. Schillinger Claudia, Petrich Annett, Lux Renate, Riep Birgit, Kikhney Judith, Friedmann Anton, Wolinsky Lawrence E., Göbel Ulf B., Daims Holger, Moter Annette, Co-Localized or Randomly Distributed? Pair Cross Correlation of In Vivo Grown Subgingival Biofilm Bacteria Quantified by Digital Image Analysis, 10.1371/journal.pone.0037583
  38. Turchin, Quantitative analysis of movement: measuring and modeling population redistribution in animals and plants (1998)