PSii Fluorescence Aggregation

This script calculates F0, Fv, Fm, and Fv/Fm values from previously calculated image thresholds. Refer to Herrit et al., 2021 for more information about pixel thresholds.

Inputs

Path to CSV containing image tresholds.

Outputs

Arguments and Flags

• Positional Arguments:
  • CSV to Process: 'csv', nargs='+'
• Required Arguments:
  • Multithreshold json file: '-m', '--multithresh'
• Optional Arguments:
  • Output directory: '-od', '--outdir', default='fluorescence_aggregation_out'
  • Classes to detect: '-of', '--outfile', default='fluorescence_aggregation'