California Current Ecosystem LTER

  1. Data catalog
  2. Datasets
  3. ALF Active and Passive Fluorescence Measurements – Station Data (CalCOFI Cruise)

ALF Active and Passive Fluorescence Measurements – Station Data (CalCOFI Cruise)

Title
Station data of passive and active fluorescence measurements of chlorophyll-a (Chl), phycoerythrin (PE), chromophoric dissolved organic matter (CDOM), and variable fluorescence (Fv/Fm) from CCE-CalCOFI Augmented cruises in the California Current System, 2012 - October 2020.

Abstract
Active and passive fluorescence measurements are made using the ALFA5 system (Chekalyuk and Hafez, 2013) on water from the ship’s underway system (these are not samples from bottles!) during CalCOFI cruises while on station. The instrument uses excitation at 405 and 510 nm to measures passively the fluorescence of chlorophyll-a (Chl), three different phycoerythrins (PE1, PE2 and PE3) and chromophoric dissolved organic matter (CDOM). Variable fluorescence (Fv/Fm) is measured actively using pump-during-probe (PDP) measurements of Chl a fluorescence induction. Fluorescence measurements are normalized to the water’s Raman fluorescence. ALF data are merged with CTD and bottle data that were collected by the CalCOFI group.
Keywords
biomass, chlorophyll, fluorescence, marine, phytoplankton, Fv/Fm, CDOM, colored dissolved organic carbon, phycobiliproteins, phycoerythrin, physiological state, pump-during-Probe

LTER Data System Record
http://dx.doi.org/10.6073/pasta/d3b2a3c539a0bb674d5f2962f167b102
Projects
California Current Ecosystem LTER

Creators
Goericke, Ralf (rgoericke@ucsd.edu)

Contact
CCE LTER Information Manager (ccelter.im@gmail.com)

Data

table ALF Active and Passive Fluorescence Measurements
Primary data table with measurements 		Rows: 1133
Columns: 37 		View / Download

Methods

Methods
The instrument used is described by Chekalyuk and Hafez (2013). A blue (b – 405 nm) and a green (g - 510 nm) laser is used to acquire data ~ four times per min. Data from files *_m.txt, *_s.txt are read into Matlab and are available for each cruise as a raw data table. Pump-During-Probe (PDP) data (*_pm.txt) are reanalyzed using a robust curve fitting procedure to generate Fv/Fm data corresponding to Fv/FmC which is generated by the ALFA5 software. Data processing involves the following: Unrealistic data (e.g. < 0 or extremely high values) are removed (set to NaN). Sections of the data that are affected by stopped flow in the UW-water system are removed as well. Data are further filtered for outliers (Matlab: isoutlier(Data.Value, 'movmean', 100, 'SamplePoints', Data.ID). Calibrations between Chl a fluorescence (CF_Rb and CF_Rg) and CalCOFI surface bottle Chl a are used to convert Chl-fluorescence measurements into predicted values of Chl a (ug-Chl/L), i.e. PredChl_b and PredChl_g. As part of this process a data file is generated that lists CalCOFI CTD and bottle data and corresponding ALFA5 data, this data product.

References

A. M. Chekalyuk and M. Hafez, "Next generation Advanced Laser Fluorometry (ALF) for characterization of natural aquatic environments: new instruments," Opt. Express 21, 14181-14201 (2013).

A. M. Chekalyuk and M. Hafez, “Advanced laser fluorometry of natural aquatic environments,” Limnol. Oceanogr. Methods 6, 591–609 (2008).

Copyright Ocean Informatics - Scripps Institution of Oceanography, UCSD © 2025