cyanoFilter: an R package to identify phytoplankton populations from flow cytometry data using cell pigmentation and granularity
Olusoji, O.D.; Spaak, J.W.; Holmes, M.; Neyens, T.; Aerts, M.; De Laender, F. (2021). cyanoFilter: an R package to identify phytoplankton populations from flow cytometry data using cell pigmentation and granularity. Ecol. Model. 460: 109743. https://dx.doi.org/10.1016/j.ecolmodel.2021.109743 In: Ecological Modelling. Elsevier: Amsterdam; Lausanne; New York; Oxford; Shannon; Tokyo. ISSN 0304-3800; e-ISSN 1872-7026, more |  |
| Author keywords | Flow cytometry; Phytoplankton; Gating; Software; Ecology |
| Authors | | Top | - Olusoji, O.D., more
- Spaak, J.W., more
- Holmes, M.
| - Neyens, T., more
- Aerts, M.
- De Laender, F., more
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| Abstract | Flow cytometry is often employed in ecology to measure traits and population size of bacteria and phytoplankton. This technique allows measuring millions of particles in a relatively small amount of time. However, distinguishing between different populations is not a straightforward task. Gating is a process in the identification of particles measured in flow cytometry. Gates can either be created manually using known characteristics of these particles, or by using automated clustering techniques. Available automated techniques implemented in statistical packages for flow cytometry are primarily developed for medicinal applications, while only two exist for phytoplankton. cyanoFilter is an R package built to identify phytoplankton populations from flow cytometry data. The package also integrates gating functions from two other automated algorithms. It also provides a gating accuracy test function that can be used to determine the accuracy of a desired gating function if monoculture flowcytometry data is available. The central algorithm in the package exploits observed pigmentation and granularity of phytoplankton cells. We demonstrate how its performance depends on strain similarity, using a model system of six cyanobacteria strains. Using the same system, we compare the performance of the central gating function in the package to similar functions in other packages. |
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