Merge pull request #42 from OceanGlidersCommunity/MOchiara-patch-1

Add DC info to chla_dmqc.md

chla.bib

@@ -89,6 +89,20 @@ @article{Hemsley2015
 pages = {11612-11621},
 year = {2015},
 doi = {10.1021/acs.est.5b00608},
-
 }
 
+@article{Xing2017,
+Author = {Xing, Xiaogang and Claustre, Herve and Boss, Emmanuel and Roesler,
+   Collin and Organelli, Emanuele and Poteau, Antoine and Barbieux, Marie
+   and D'Ortenzio, Fabrizio},
+Title = {Correction of profiles of in-situ chlorophyll fluorometry for the
+   contribution of fluorescence originating from non-algal matter},
+Journal = {LIMNOLOGY AND OCEANOGRAPHY-METHODS},
+Year = {2017},
+Volume = {15},
+Number = {1},
+Pages = {80-93},
+Month = {JAN},
+DOI = {10.1002/lom3.10144},
+ISSN = {1541-5856},
+}

sections/chla_dmqc.md

@@ -1,10 +1,10 @@
 (dmqc)=
 # Delayed Mode Quality Control
 
-Text
-
 ### Dark count re calibration
 
+As mentioned in {numref}`mission-execution`, inter-calibrations between the gliders and CTD fluorescence sensors together with bottle samples of chlorophyll a are a fundamental tool in post recovery data processing. Additionally, to this, a further dark count correction is recommended when possible. Assuming no fluorescence signal in deeper waters, a deep-offset correction can be estimated. This is computed using the mean deep fluorescence (the deeper, the better) and can be subtracted from the data and used to further correct the results. This can be complex especially in study areas characterized by shallow waters, heavy resuspension, and overall complexity of the optical properties of the water column. Furthermore, when assessing this deep dark count offset, the contribution of deep sea red fluorescence on in situ dark counts should be determined. This can be done if the glider is equipped with reliable FDOM sensors {cite}`Xing2017`.
+
 ### 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.