Update chla_dmqc.md

_config.yml

@@ -33,4 +33,4 @@ sphinx:
 
 bibtex_reference_style      : author_year_round
 bibtex_default_style        : myapastyle
-bibtex_bibfiles             : oxygen.bib
+bibtex_bibfiles             : chla.bib

chla.bib

@@ -6,8 +6,89 @@ @article{NicholsonFeen2017
 number = {5},
 pages = {495-502},
 doi = {https://doi.org/10.1002/lom3.10177},
-url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lom3.10177},
-eprint = {https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lom3.10177},
 abstract = {Abstract An Aanderaa Data Instruments 4831 oxygen optode was configured on an underwater glider such that the optode extended into the atmosphere during each glider surface interval enabling in situ calibration of the sensor by directly measuring the known oxygen partial pressure of the atmosphere. The approach, which has previously been implemented on profiling floats but not on gliders, was tested during a 15-d deployment at the New England shelf break in June 2016, a productive period during which surface O2 saturation averaged 110\%. Results were validated by shipboard Winkler O2 calibration casts, which were used to determine a sensor gain factor of 1.055 ± 0.004. Consistent with profiling float observations, air measurements contain contamination from splashing water and/or residual seawater on the sensor face. Glider surface measurements were determined to be a linear combination of 36\% of surface water and 64\% atmospheric air. When correcting air measurements for this effect, a sensor gain correction of 1.055 ± 0.005 was calculated based on comparing glider air measurements to the expected atmospheric pO2 calculated from atmospheric pressure and humidity data from a nearby NOAA buoy. Thus, the two approaches were in agreement and were both demonstrated to be accurate to within ±0.5\%. We expect uncertainty in the air-calibration could be further reduced by increasing the vertical positioning of the optode, lengthening deployment time, or operating in waters with surface O2 saturation closer to equilibrium.},
 year = {2017}
 }
+
+}
+
+@article{Thomalla2018,
+author = {Thomalla, Sandy J. and Moutier, William and Ryan-Keogh, Thomas J. and Gregor, Luke and Schütt, Julia},
+title = {An optimized method for correcting fluorescence quenching using optical backscattering on autonomous platforms},
+journal = {Limnology and Oceanography: Methods},
+volume = {16},
+number = {2},
+pages = {132-144},
+doi = {https://doi.org/10.1002/lom3.10234},
+abstract = {Abstract Autonomous platforms will begin to address the space-time gaps required to improve estimates of phytoplankton distribution, which will aid in the quantification of baseline conditions necessary to detect long-term trends that can be attributed to factors such as climate change. However, there is a need for high quality controlled and verified datasets. In vivo fluorescence provides a proxy for chlorophyll pigment concentration, but it is sensitive to physiological downregulation under incident irradiance (fluorescence quenching). Quenching can undermine the validity of these datasets by underestimating daytime fluorescence derived chlorophyll across regional and temporal scales. Existing methods from the literature have corrected for quenching, however, these methods require certain assumptions to be made that do not hold true across all regions and seasons. The method presented here overcomes some of these assumptions to produce corrected surface fluorescence during the day that closely matched profiles from the previous (or following) night, decreasing the difference to less than 10\%. This method corrects daytime quenched fluorescence using a mean nighttime profile of the fluorescence to backscattering ratio multiplied by daytime profiles of backscattering from the surface to the depth of quenching (determined as the depth at which the day fluorescence profile diverges from the mean night profile). This method was applied to a 7-month glider time series in the sub-Antarctic Southern Ocean together with four other methods from the literature for comparison. In addition, the method was applied to a glider time series from the North Atlantic to demonstrate its applicability to other ocean regions.},
+year = {2018}
+}
+
+@article{Xing2012,
+author = {Xing, Xiaogang and Claustre, Hervé and Blain, Stéphane and D'Ortenzio, Fabrizio and Antoine, David and Ras, Josephine and Guinet, Christophe},
+title = {Quenching correction for in vivo chlorophyll fluorescence acquired by autonomous platforms: A case study with instrumented elephant seals in the Kerguelen region (Southern Ocean)},
+journal = {Limnology and Oceanography: Methods},
+volume = {10},
+number = {7},
+pages = {483-495},
+doi = {https://doi.org/10.4319/lom.2012.10.483},
+abstract = {As the proxy for Chlorophyll a (Chl a) concentration, thousands of fluorescence profiles were measured by instrumented elephant seals in the Kerguelen region (Southern Ocean). For accurate retrieval of Chl a concentrations acquired by in vivo fluorometer, a two-step procedure is applied: 1) A predeployment intercalibration with accurate determination by high performance liquid chromatography (HPLC) analysis, which not only calibrates fluorescence in appropriate Chl a concentration units, but also strongly reduces variability between fluorometers, and 2) a profile-by-profile quenching correction analysis, which effectively eliminates the fluorescence quenching issue at surface around noon, and results in consistent profiles between day and night. The quenching correction is conducted through an extrapolation of the deep fluorescence value toward surface. As proved by a validation procedure in the Western Mediterranean Sea, the correction method is practical and relatively reliable when there is no credible reference, especially for deep mixed waters, as in the Southern Ocean. Even in the shallow mixed waters, the method is also effective in reducing the influence of quenching.},
+year = {2012}
+}
+
+
+@article{ Biermann2015,
+Author = {Biermann, L. and Guinet, C. and Bester, M. and Brierley, A. and Boehme,
+   L.},
+Title = {An alternative method for correcting fluorescence quenching},
+Journal = {OCEAN SCIENCE},
+Year = {2015},
+Volume = {11},
+Number = {1},
+Pages = {83-91},
+DOI = {10.5194/os-11-83-2015},
+ISSN = {1812-0784},
+ResearcherID-Numbers = {Bester, Marthán N/E-5387-2010
+   Guinet, Christophe/AAR-8457-2020
+   Brierley, Andrew/G-8019-2011
+   Boehme, Lars/B-6567-2009
+   },
+ORCID-Numbers = {Brierley, Andrew/0000-0002-6438-6892
+   Boehme, Lars/0000-0003-3513-6816
+   Biermann, Lauren/0000-0002-6995-7586},
+Unique-ID = {WOS:000350556600006},
+}
+
+
+@article{ Swart2015,
+Author = {Swart, S. and Thomalla, S. J. and Monteiro, P. M. S.},
+Title = {The seasonal cycle of mixed layer dynamics and phytoplankton biomass in
+   the Sub-Antarctic Zone: A high-resolution glider experiment},
+Journal = {JOURNAL OF MARINE SYSTEMS},
+Year = {2015},
+Volume = {147},
+Number = {SI},
+Pages = {103-115},
+Month = {JUL},
+DOI = {10.1016/j.jmarsys.2014.06.002},
+ISSN = {0924-7963},
+EISSN = {1879-1573},
+ResearcherID-Numbers = {Thomalla, Sandy/AAS-4133-2021
+   Swart, Sebastiaan/U-5498-2017},
+ORCID-Numbers = {Swart, Sebastiaan/0000-0002-2251-8826},
+Unique-ID = {WOS:000356547200012},
+}
+
+
+@article{Hemsley2015,
+author = {Hemsley, Victoria S. and Smyth, Timothy J. and Martin, Adrian P. and Frajka-Williams, Eleanor and Thompson, Andrew F. and Damerell, Gillian and Painter, Stuart C.},
+title = {Estimating Oceanic Primary Production Using Vertical Irradiance and Chlorophyll Profiles from Ocean Gliders in the North Atlantic},
+journal = {Environmental Science \& Technology},
+volume = {49},
+number = {19},
+pages = {11612-11621},
+year = {2015},
+doi = {10.1021/acs.est.5b00608},
+
+}
+

sections/chla_dmqc.md

@@ -2,3 +2,24 @@
 # Delayed Mode Quality Control
 
 Text
+
+### Dark count re calibration
+
+### Non photochemical quenching corrections
+
+Fluorescence data has to be corrected for non-photochemical quenching (NPQ) in most cases. NPQ is a physiological response to high light environments used by plants and algae to protect themselves from damage and causes an evident weakening in fluorescence signal during the day. NPQ occurs only during the daytime or whenever light avaialbility is high, therefore when night measurements close in time and space are available, they can be used to correct daytime profiles. Different methods exist for NPQ the paper by {cite}`Thomalla2018` provides a good overview on the various methodologies. 
+The most suitable methodology will vary based on the study area as well as the research question. The assumptions and corrections of each method may not provide credible results for the diffent water column structures so the methodology has to be chosen carefully.
+
+Shall we add the nice table from the Thomalla paper summrizing all the methodologes? I add the draft below
+
+| Study  |  Equation | Assumptions | 
+|---|---|---|
+| {cite}`Xing2012`  | 	C1 = max<sub>0≤z≤MLD</sub> (Fl(z)) <br> Flc(z) = C1; 0≤z≤d(C1)| - Fluorescence uniform within MLD  <br> - No quenching below max fluorescence within MLD |
+| {cite}`Biermann2015` |  C2 = max<sub>0≤z≤ED</sub> (Fl(z)) <br> Flc(z) = C2; 0≤z≤d(C2) |  - Fluorescence within ED uniform |
+| {cite}`Swart2015`  | C3 = max<sub>0≤z≤ED</sub> $\left(\frac{Fl}{b_{bp}}\right)$ <br> Flc(z) = C3 × b<sub>bp</sub>(z); 0≤z≤d(C3) | - fl : bbp ratio constant with depth |
+| {cite}`Hemsley2015`  | Chl<sub>NT</sub> = m × $b_{{bp}_{NT}}$ + c*  <br> Chl<sub>DT</sub>(z) = m × b<sub>bp</sub>(z)<sub>DT</sub> + c; 0≤z≤ED <br> *m (slope) and c (intercept) | - fl : bbp ratio constant with depth and time |
+| {cite}`Thomalla2018`  |  Flc<sub>DT</sub> = $\left(\frac{Fl_{NT}(z)}{Fl_{DT}(z)}\right)$ × b<sub>bp</sub>(z)<sub>DT</sub>; 0≤z≤QD <br> If Flc<sub>DT</sub>(z) < Flc<sub>DT</sub>(z) then no correction is applied |  - Same depth distribution of fl : bbp between night and day <br> - No quenching at night |
+
+**b<sub>bp</sub>**: particulate backscattering profile; **d**: depth; **DT**: daytime profile; **ED**: euphotic zone depth; **Fl**: fluorescence profile; **Flc**: corrected fluorescence profile; **FlNT**: averaged fluorescence over the night; **MLD**: mixed layer depth; **NT**: nighttime profile; **QD**: quenching depth; **z**: depth domain
+
+We can say that if day and night profiles are used, the sunset/sunrise time can be used to separate the profiles or if PAR is available, this variable can used instead