Summarize biovolumes and carbon content from IFCB data

This function calculates aggregated biovolumes and carbon content from Imaging FlowCytobot (IFCB) samples based on feature and MATLAB classification result files, generated by the code in `ifcb-analysis` repository (Sosik and Olson 2007). Biovolumes are converted to carbon according to Menden-Deuer and Lessard 2000 for individual regions of interest (ROI), where different conversion factors are applied to diatoms and non-diatom protist. If provided, it also incorporates sample volume data from HDR files to compute biovolume and carbon content per liter of sample.

ifcb_summarize_biovolumes(
  feature_folder,
  class_folder,
  hdr_folder = NULL,
  micron_factor = 1/3.4,
  diatom_class = "Bacillariophyceae",
  threshold = "opt"
)

Arguments

feature_folder

Path to the folder containing feature files (e.g., CSV format).

class_folder

Path to the folder containing class files (e.g., MATLAB MAT format).

hdr_folder

Path to the folder containing HDR files (optional).

micron_factor

Conversion factor from microns per pixel (default: 1/3.4).

diatom_class

A string vector of diatom class names in the World Register of Marine Species (WoRMS). Default is "Bacillariophyceae".

threshold

Threshold for classification (default: "opt").

Value

A data frame summarizing aggregated biovolume and carbon content per class per sample. Columns include 'sample', 'class', 'biovolume_mm3', 'carbon_ug', 'ml_analyzed', 'biovolume_mm3_per_liter', and 'carbon_ug_per_liter'.

Details

This function performs the following steps: 1. Extracts biovolumes and carbon content from feature and class files using `ifcb_extract_biovolumes`. 2. Optionally incorporates volume data from HDR files to calculate volume analyzed per sample. 3. Computes biovolume and carbon content per liter of sample analyzed.

References

Menden-Deuer Susanne, Lessard Evelyn J., (2000), Carbon to volume relationships for dinoflagellates, diatoms, and other protist plankton, Limnology and Oceanography, 3, doi: 10.4319/lo.2000.45.3.0569.

Sosik, H. M. and Olson, R. J. (2007), Automated taxonomic classification of phytoplankton sampled with imaging-in-flow cytometry. Limnol. Oceanogr: Methods 5, 204–216.

Examples

if (FALSE) {
# Example usage:
ifcb_summarize_biovolumes("path/to/features", "path/to/class", hdr_folder = "path/to/hdr")
}