Dataset Open Access

Dataset: Quantifying cell densities and biovolumes of phytoplankton communities and functional groups using scanning flow cytometry, machine learning and unsupervised clustering

Thomas, Mridul K.; Fontana, Simone; Reyes, Marta; Pomati, Francesco

This dataset contains all relevant data for the manuscript (in submission) "Quantifying cell densities and biovolumes of phytoplankton communities and functional groups using scanning flow cytometry, machine learning and unsupervised clustering".

Code written to analyse this dataset (which may be adapted for other flow cytometry datasets) is found at https://zenodo.org/record/999747

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Naming convention for raw flow cytometry data files (located in /Script 3. Generating raw data subset/input/):

[Allparameters] _ [Year] - [Month] - [Date]  [Hour] [u] [Minute] _ [Depth]

e.g: Allparameters_2014-07-31 08u08_1.0m

The date, time and depth indicate the location and time at which the measurement was taken.

We are presently using this dataset for multiple publications that are in preparation. To avoid duplicated efforts, we request that you contact the authors if you are interested in pursuing a research project with this data. Contact information: Mridul K. Thomas - mrit {at} dtu {dot} dk Francesco Pomati - francesco {dot} pomati {at} eawag {dot} ch
Files (8.6 GB)
Name Size
Script 1. Training biovolume estimation.zip
md5:83803a569b10da0a5cfd9470a9093d7f 		3.5 MB Download
Script 2. Identifying important variables for data cleaning.zip
md5:3a95df2dfd1b74d7f1c0d8cbfbaf8920 		11.1 MB Download
Script 3. Generating raw data subset.zip
md5:47f082290386235c81547557f5fc92df 		8.2 GB Download
Script 4. Cleaning by clustering.zip
md5:19c8ffdd62d569e33731f5662db1f474 		310.1 MB Download
Script 5. Generating cleaned data subset.zip
md5:edf2bf072e05db7d59bdf4ed7ab1bd87 		39.3 MB Download
Script 6. Calculating cell density.zip
md5:3b4ed742c96e7d46b8128af8b6597655 		8.3 kB Download
Script 7. Identifying important variables for group distinction.zip
md5:f18128da04aa6bad6473493a73524ee0 		24.6 MB Download
Script 8. Calculating cell densities of clusters.zip
md5:cbd29e56442a2798bc1b9438af98bd67 		87.2 kB Download
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Publication date:
September 28, 2017
DOI:
10.5281/zenodo.977773

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Keyword(s):
phytoplankton, flow cytometry, automated monitoring, traits
License (for files):
Creative Commons Attribution 4.0 International

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Version 1 10.5281/zenodo.977773 Sep 28, 2017
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