1. Data Processing of IOP Packages Attenuation, Absorption and Backscattering c, a, b b Ian Walsh, Ph.D. Director of Science, Sea-Bird Scientific

2. ©2014 Sea-Bird Scientific Inc. Data Processing of IOP Packages Review of IOP theory Description of ac-s in-situ spectrophotometer ac meter protocol Calibration overview Collecting data with WETview Scattering Correcting absorption data Backscattering NTU to Backscattering calibration conversion

3. ©2014 Sea-Bird Scientific Inc. Data Processing of IOP Packages Review of IOP theory Description of ac-s in-situ spectrophotometer ac meter protocol Calibration overview Collecting data with WETview Scattering Correcting absorption data Backscattering NTU to Backscattering calibration conversion

4. ©2014 Sea-Bird Scientific Inc. I = I 0 e -cz I0I0 I z Beer’s Law

5. ©2014 Sea-Bird Scientific Inc. c, attenuation coefficient (m -1 ) a, absorption coefficient (m -1 ) b, scattering coefficient (m -1 ) Relationships: c = a + b c t = c part + c diss + c w a t = a part + a diss + a w b t = b part + b w Components of Light Attenuation: Absorption and Scattering

6. ©2014 Sea-Bird Scientific Inc. Measuring a and c: WET Labs ac-s Measures absorption (a) and attenuation (c) Dual flow path design Wavelengths from 400-730 nm with 4 nm resolution 10 and 25 cm path lengths 4 Hz sampling rate 500 or 5000 m depth rating filter wheel Linear Variable Filters (LVFs)

7. ©2014 Sea-Bird Scientific Inc. Transmissometer ll 00 l Collimating optics Collimating optics

8. ©2014 Sea-Bird Scientific Inc. Reflective tube Air gap or reflective surface Flow cell cover adapted from Zaneveld et al. 1992 Forward scattered light from ~0 to 41.7 degrees is included in the signal measured by the detector Reflective Tube Absorption Meter Design

9. ©2014 Sea-Bird Scientific Inc. ac-s Cross-Section

10. ©2014 Sea-Bird Scientific Inc. Theoretical Uncertainty ~0.0001 m -1 in waters with low attenuation Estimated Effective Uncertainty ~0.002 to 0.005 m -1 in waters with low attenuation Wavelength dependent  nm needs longer integration time to achieve high precision ac-s Performance

11. ©2014 Sea-Bird Scientific Inc. Data Processing of IOP Packages Review of IOP theory Description of ac-s in-situ spectrophotometer ac meter protocol Calibration overview Collecting data with WETview Scattering Correcting absorption data Backscattering NTU to Backscattering calibration conversion

12. ©2014 Sea-Bird Scientific Inc. LEGEND t - total w - water  - phytoplankton d - non-algal particles p – particulate material g – dissolved material cwcw Clean Water: Field and lab calibrations track instrument changes between factory services. Follow WET Labs protocol document available on WET Labs website: http://www.wetlabs.com/sites/default/files /documents/acprotq.pdf Calibrating ac-s: Factory calibration defines c w

13. ©2014 Sea-Bird Scientific Inc. Water calibrations Optically clean water Pre-use (lab) and regularly during field use Record values for ~30 s and average to obtain calibration values Replicate and track over time For the most accurate measurements, calibrations are required to compensate for drift, i.e., scaling factors (F) vary over time.

14. ©2014 Sea-Bird Scientific Inc. cwcw Use deep or clean water to establish nominal c w : Assume clean water values for particle components are low and constant in space and time Use clean water values as additional offset in post processing Field Calibration of ac-s Depth c measured

15. ©2014 Sea-Bird Scientific Inc. LEGEND t - total w - water  - phytoplankton d - non-algal particles p – particulate material g – dissolved material Define minimum at depth z Depth c measured

16. ©2014 Sea-Bird Scientific Inc. LEGEND t - total w - water  - phytoplankton d - non-algal particles p – particulate material g – dissolved material Adjust all profiles Depth c adj

17. ©2014 Sea-Bird Scientific Inc. LEGEND t - total w - water  - phytoplankton d - non-algal particles p – particulate material g – dissolved material Filter All Particles out of the Water Use a 0.2 um or 0.4 um filter Assume absorption due to dissolved species is a constant Works very well with underway systems Calibrating with filtered water c measured Depth

18. ©2014 Sea-Bird Scientific Inc. “Dissolved” measurement 0.2 micron pore-size filter on intake. High flow rates Pall Suporcap/Maxi-cap Pre-soak or flush with deionized water a and/or c, as b g = 0.0, c g = a g 2 ac ’ s, or consecutive casts Results in reduced flow rate Mixing in filter smears gradients in a g Profiling: slow decent rate Must lag correct profile data

19. ©2014 Sea-Bird Scientific Inc. Data Processing of IOP Packages Review of IOP theory Description of ac-s in-situ spectrophotometer ac meter protocol Calibration overview Collecting data with WETview Scattering Correcting absorption data Backscattering NTU to Backscattering calibration conversion

20. ©2014 Sea-Bird Scientific Inc. WETview Data Acquisition System Click to Open Device File ac-s should be connected and powered

21. ©2014 Sea-Bird Scientific Inc. Open Device File Click to Open Device File Device files are:.dev for water.cal for air

22. ©2014 Sea-Bird Scientific Inc. Open Device File Directory will open at program location Change location folder, e.g. calibration tracking or cruise data folder

23. ©2014 Sea-Bird Scientific Inc. Select Communication Port

24. ©2014 Sea-Bird Scientific Inc. Start Acquiring Data Click to start collecting data Data files are saved when you are done collecting data

25. ©2014 Sea-Bird Scientific Inc. Data View

26. ©2014 Sea-Bird Scientific Inc. Save Data Directory will open at program location

27. ©2014 Sea-Bird Scientific Inc. Save Data Change location folder, e.g. calibration tracking or cruise data folder

28. ©2014 Sea-Bird Scientific Inc. WETview Calibration To start a calibration, Select Configure in the File menu Start process after data variance is minimized. Save Data Set, then Configure

29. ©2014 Sea-Bird Scientific Inc. WETview Calibration 1.Stabilize signal 2.Save data 3.Auto Cal

30. ©2014 Sea-Bird Scientific Inc. WETview Calibration

31. ©2014 Sea-Bird Scientific Inc. WETview Calibration 1.Data Collection Counting 2.Save New Device File

32. ©2014 Sea-Bird Scientific Inc. WETview Calibration Recommend using a date in the file name for tracking purposes Note, do not overwriting the previous.cal or.dev files!.cal files for air calibrations.dev files for water calibrations

33. ©2014 Sea-Bird Scientific Inc. WETview Calibration Data after the.cal file is used

34. ©2014 Sea-Bird Scientific Inc. Device File Annotated Calibration File ACS Meter 53000067 ; Serial number 3; structure version number tcal: 20.4 C, ical: 21.3 C. The offsets were saved to this file on 10/21/11. 00 ; Depth calibration 115200 ; Baud rate 0.25 ; Path length (meters) 79 ; output wavelengths 36 ; number of temperature bins 3.58234.3813645.470616.4927.472203 C398.9A400.981.765140.556434-0.053294-0.042208-0.037851-0.035375 C403.7A405.0101.7151540.680489-0.048162-0.037653-0.031775-0.031118 C407.6A408.9111.6558140.766596-0.040607-0.030697-0.025398-0.024145 C412.1A412.6121.594090.819793-0.035592-0.026248-0.021001-0.019391 C416.2A416.9131.5247380.851991-0.03086-0.024106-0.019847-0.018846 C421.0A421.7151.4648430.872155-0.024519-0.018606-0.015533-0.014885 C425.8A426.3161.4183020.890925-0.02176-0.016814-0.014411-0.013019 C430.4A431.1171.3734110.907548-0.018204-0.014427-0.012378-0.012059 C434.7A435.2181.3273190.924527-0.014153-0.010815-0.009802-0.009154 C438.9A439.6201.2925390.940059-0.01463-0.010965-0.009792-0.008929 C443.9A444.2211.2629590.956568-0.013204-0.010061-0.008488-0.007745 C448.6A449.2221.2370.973888-0.013317-0.0099-0.008602-0.007673 C453.8A454.1231.2126570.991515-0.013188-0.009598-0.008143-0.007092 C458.5A458.9LtBlue1.1877951.010199-0.012065-0.008582-0.00727-0.006473 C463.3A463.4261.164461.029494-0.011997-0.008543-0.006866-0.006195 C468.0A468.4271.1507931.047945-0.011844-0.008555-0.007142-0.006498

35. ©2014 Sea-Bird Scientific Inc. Data Processing of IOP Packages Review of IOP theory Description of ac-s in-situ spectrophotometer ac meter protocol Calibration overview Collecting data with WETview Scattering Correcting absorption data Backscattering NTU to Backscattering calibration conversion

36. ©2014 Sea-Bird Scientific Inc. NTU Calibration to Backscattering The bead to formazin calibration relationship has been linked and conversion coefficients produced. WavelengthNTU to Beta 4120.0099378 4400.0105935 4700.0097312 4880.0087152 5100.0073748 5320.0062665 5950.0041454 6500.0032033 6760.0029309 7000.0027272 7150.0026079 7200.0025677 7300.0024849 8800.0020546 Backscattering instruments with wide ranges for inland waters were supplied with NTU calibrations Caution: these coefficients are only for ECO backscattering sensors, they do not apply to any other turbidity sensors

37. ©2014 Sea-Bird Scientific Inc. NTU Calibration to Backscattering To convert the NTU scale factor to backscattering scale factor: NTU Scale Factor from characterization sheet: NTU SF = 0.2427 NTU/count For 700 nm

38. ©2014 Sea-Bird Scientific Inc. NTU Calibration to Backscattering Multiply NTU SF by Beta conversion factor: Beta SF = 0.027272 ( m -1 sr -1 )/NTU * 0.2427 NTU/count = 0.00662 m -1 sr -1 WavelengthNTU to Beta 4120.0099378 4400.0105935 4700.0097312 4880.0087152 5100.0073748 5320.0062665 5950.0041454 6500.0032033 6760.0029309 7000.0027272 7150.0026079 7200.0025677 7300.0024849 8800.0020546

39. ©2014 Sea-Bird Scientific Inc. Data Processing of IOP Packages Review of IOP theory Description of ac-s in-situ spectrophotometer ac meter protocol Calibration overview Collecting data with WETview Scattering Correcting absorption data Backscattering NTU to Backscattering calibration conversion

40. ©2014 Sea-Bird Scientific Inc. Scattering correction of absorption Pegau, et al., 2003, Ocean Optics Protocols for satellite ocean color sensor validation, Revision 4, Volume IV, NASA/TM-2003 Error in reflective tube due to incomplete capture of scattered light Filtered absorption measurement correction not needed (b g = 0.0 )

41. ©2014 Sea-Bird Scientific Inc. Scattering correction of absorption Methods 1.a TS m (715 nm) subtraction: null wavelength 2.Assume constant proportion of scattering (14% of b) 3.Variable proportion of scattering Iterative process Dependent on good calibrations Noisy data must be smoothed Compare between methods Use of dissolved a g to compute a p to check corrections

42. ©2014 Sea-Bird Scientific Inc. Method 1 – subtraction of NIR null wavelength a pg (l) = a TS m (l) – a TS m (NIR) NIR ~ 710 750 nm Assumptions: The shape and magnitude of the VSF is independent of l No absorption by any materials in NIR Scattering error the same for all wavelengths Advantages: Allows for changes as a function depth and particle type Uses data from the a side only Scattering correction of absorption

43. ©2014 Sea-Bird Scientific Inc. Scattering correction of absorption Method 2 – Constant proportion of b a pg (l) = a TS m (l) – Y [c TS m (l) - a TS m (l)] Assumptions: The shape of the VSF is independent of l and type of particles Scattering error the same for all wavelengths Advantages: Allows for changes as a function of depth, but not particle type If NIR channel is unavailable, or if no TS data available  varies from ~ 0.14 for predominately biological particles (open ocean) to 0.18 in waters where scattering dominated by suspended particles (Case 2). Smooth b before correcting

44. ©2014 Sea-Bird Scientific Inc. Method 3 – varying proportion of b a pg ( ) = a TS m ( ) –  NIR [c TS m ( ) - a TS m ( )] Assumptions: Shape of VSF independent of Advantages: Allows for changes as a function of depth and particle type Disadvantage: Requires multiple measurements, thus easy to induce noise in absorption data. Smooth  and b before correcting.  NIR should be between 0.07 and 0.35 where  NIR = a TS m (NIR) / [c TS m (NIR) - a TS m (NIR)] Scattering correction of absorption

45. ©2014 Sea-Bird Scientific Inc. Data collection Strongly recommended to collect CTD data Provides hydrographic information for interpretation Needed for temperature and salinity corrections of ac data Data acquisition system – multiple instruments Control sampling and power Store, integrate, and real-time output of data

46. ©2014 Sea-Bird Scientific Inc. Processing steps 1.Apply instrument calibration a.Factory Calibration b.Field Calibration 2.Profiling: Lag offset 3.Apply temperature and salinity corrections 4.Scattering correction of total absorption data 5.Binning 6.Derived parameters 7.Quality control

47. ©2014 Sea-Bird Scientific Inc. Merge with CTD data Profiling: Interpolation to ac-s resolution Time stamps of instruments Depth adjustment – pressure Binning or averaging? Depends on resolution you want Reduces the variability

48. ©2014 Sea-Bird Scientific Inc. Lag corrections Profiling systems Lag between hydrographic data and ac data Flushing time of flow tube volume Function of tubing length, pump speed, flow rate Filter reduces flow rate, increases the lag Approaches to correct data 1.Direct: Measure flow rate in ac using flow meter Requires estimating the volume of the intake tubing, and the relative position of the intakes to the ac sample tubes. 2.Indirect: NIR dependence on temperature Multiple casts with different decent rates.

49. ©2014 Sea-Bird Scientific Inc. Temperature & salinity correction Pegau & Zaneveld 1993 30 o C 5oC5oC a water (m - 1 ) ~0.003 m -1 deg -1 At 715 nm ~ -0.0002 m -1 PSU -1 Absorption and beam attenuation properties of pure water vary as a function of temperature and salinity. Must correct in relation to the properties of pure water at the time of calibration Salinity Temperature Temperature affects absorption NOT scattering (minimal) Thus same affects on a and c Salinity affects absorption AND scattering differently Thus different affects on a and c

50. ©2014 Sea-Bird Scientific Inc. Temperature & salinity correction Calibration Temperature (T t ): pure water in flow tubes during calibration. Provided in device file from WET Labs Must measure the temperature during your pure water calibration Salinity (S): (recall that pure water = 0.0 PSU). Coefficients in: Pegau, et al., 1997, Absorption and attenuation of visible and near-infrared light in water: dependence on temperature and salinity, Appl. Opt., 36(24): 6035-6046.

51. ©2014 Sea-Bird Scientific Inc. Binning Depends on application and desired resolution You may want to bin BEFORE processing to simplify. Independence of samples: Flow in ac not laminar. Takes one complete flushing time to obtain an independent sample. Increased flushing time with filtered measurements. Between flow tubes (a and c). Two separate sample volumes. Occurrence of rare large particles in one tube and not the other. At typical pump speeds, best resolution 0.3 m, or at least 2 seconds of data. Binning Median: minimize the influence of rare particles, especially when using a and c measurements together. Average: check sample distribution, normal?