Turner Designs C3 User manual

January 27, 2009
P/N: 998-2300
Revision C
TURNER DESIGNS
845 W. Maude Ave.
Sunnyvale, CA 94085
Phone: [phone]
FAX: [phone]

C3 Submersible Fluorometer
Table of Contents
Table of Contents ...................................................................................................................................2
1.0 Introduction .............................................................................................................................3
2.0 Inspection and Setup........................................................................................................................4
2.1 Instrument Checklist....................................................................................................................4
3.0 C-Soft Windows ™ User Interface .................................................................................................... 7
3.1 Software Installation and PC Requirements................................................................................7
3.1.1 Minimum PC Requirements........................................................................7
3.1.2 Software Installation ...................................................................................7
3.1.3 PC Software Interface .................................................................................8
3.2 Software Operation......................................................................................................................8
3.2.1 Settings Screen............................................................................................8
3.2.2 Current Data and Calibration Screen...........................................................9
3.2.3 Log Setup Screen ......................................................................................15
3.2.4 Downloading and File Management .........................................................16
3.2.5 Integrating the C3 Submersible Fluorometer to a Third Party Platform...17
4.0 Deployment & Accessories.............................................................................................................20
4.1 Connecting the Submersible Battery Pack ................................................................................20
4.2 Battery Bracket Installation.......................................................................................................20
4.3 Installing the Mechanical Wiper................................................................................................20
4.4 Installing the Flow Cap ............................................................................................................. 21
4.5 Using the Secondary Solid Standard .........................................................................................22
Important Note Regarding Use of Fluorescein Sensor....................................................................24
5.0 Maintenance and Warranty............................................................................................................25
5.1 Maintenance ..............................................................................................................................25
5.1.1 Rinsing ......................................................................................................25
5.1.2 Care for the bulkhead connector ...............................................................25
5.2 Warranty Service.......................................................................................................................25
5.2.1 Out-of-Warranty Service...........................................................................25
Appendix A. C3 Submersible Fluorometer Specifications....................................................................27
Appendix B. C3 Submersible Fluorometer Operating Instructions......................................................28
Appendix C. C3 Submersible Fluorometer Wiring Guide.................................................................... 29
Appendix D. Secondary Standard - In Vivo Chlorophyll a & Rhodamine Dye Applications...............30

C3 Submersible Fluorometer
1.0 Introduction
The C3 Submersible Fluorometer is manufactured according to user’s optical specifications
with one, two, or three optical sensors ranging in wavelengths from ultra violet to infrared.
Each optical sensor is designed with a static excitation and emission filter. The C3
Submersible Fluorometer comes with a factory installed temperature probe and can be
configured with a pressure sensor for depth measurements up to 600 meters and/or a wiper
motor to minimize biofouling during extended or short-term deployments. The C3
Submersible Fluorometer Windows™based user interface allows for easy calibration of each
sensor, digital data reporting, data logging, file downloading, and digital export of data.
Available Optical Sensors:
♦Turbidity
♦In Vivo Chlorophyll a
♦Blue Green Algae (Phycoerythrin)
♦Blue Green Algae (Phycocyanin)
♦CDOM
♦Crude Oil
♦Fluorescein (See important note on page 25)
♦Rhodamine Dye
♦Optical Brighteners
♦Custom Optics
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2.0 Inspection and Setup
2.1 Instrument Checklist
The C3 Submersible Fluorometer package (P/N: 2300-000) includes:
♦C3 Submersible Fluorometer
♦Factory installed temperature sensor
♦Interface cable for PC with 12V power supply
♦CD includes C-Soft software, user’s manual, and quick start guide
Temperature Sensor
12V power supply
Computer interface cable
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Optional Accessories:
♦Pressure sensor (P/N: 2300-360) Factory installed
♦C3 Mechanical Wiper (P/N: 2300-450) Factory installed
Note: The Pressure sensor and mechanical wiper can only be installed during the
production of the unit
♦Replaceable Brush (P/N: 2200-460)
♦Submersible Battery Kit includes charger (P/N: 2200-601)
♦C3 Submersible Battery Bracket (P/N: 2300-603)
♦Flow Cap (P/N: 2300-700)
♦Shade Cap (P/N: 2300-500)
♦Shade Cap Weight (P/N: 2300-510)
♦Booster Kit (P/N: 2200-900)
Note: Booster Kits are required for cable lengths greater than 5 meters.
♦Extended Cables:
♦10 meters (P/N: 105-2595)
♦25 meters (P/N: 105-2596)
♦50 meters (P/N: 105-2597)
♦Custom lengths available upon request
♦Secondary solid standard (P/N: 2300-900) for multiple sensors
Note: Solid Standards are not available for turbidity or ultraviolet sensors
Mechanical Wiper Submersible Battery
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Battery Bracket
Solid Standard Insert
Secondary Solid Standard
Flow Cap Shade Cap
Booster Kit
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Identification
Sensors labeled 1, 2, or 3 adjacent to the optics on the face of the C3 Submersible
Fluorometer correspond to channels 1, 2, and 3 in the C3 Windows Software.
Note: The channel labels can be modified in the C-Soft software.
Light emitting diode color table.
Application Light Source Color
Chlorophyll a Blue
Turbidity Infra Red (No Color)
Phycocyanin Yellow
Phycoerythrin Green
Fluorescein Blue (See important note on page 25)
Rhodamine Green
CDOM Ultra Violet (No Color)*
Crude Oil Ultra Violet (No Color)*
Optical Brighteners Ultra Violet (No Color)*
*Do not look directly onto the optics. Ultraviolet light can be damaging to the eyes.
3.0 C-Soft Windows™User Interface
The C-Soft Windows™based user interface allows for intuitive calibration, data logging set
up, and file downloading.
3.1 Software Installation and PC Requirements
3.1.1 Minimum PC Requirements
♦133MHz microprocessor
♦600 X 800 VGA resolution
♦Microsoft Windows™98
♦32 MB RAM
3.1.2 Software Installation
1. Exit all Windows™programs
2. Insert the C-Soft CD (also located on the Turner Designs Software web page,
http://www.turnerdesigns.com/t2/sw/main.html).
3. Open the C-Soft software folder and double click on the setup icon.
4. Double click on the “setup.exe” icon to begin installation.
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5. The software will automatically be installed in the PC’s (C:/Program Files/C-Soft)
folder unless user selects alternate location.
6. After restarting the PC double click on the "C-Soft" icon located on the desktop.
C-Soft Note: You may receive a warning message asking if you want to unblock messages,
select "Unblock"
3.1.3 PC Software Interface
1. Connect the 9-pin serial end of the interface cable to the serial port on the back of the
PC.
Note: If your computer only has USB ports we recommend purchasing a USB to serial
adapter cable. (See Turner Designs Support web page for recommendations)
2. Connect the 8-pin female end of the interface cable to the 8-pin male connector on the
C3 Submersible Fluorometer.
3. Connect the interface cable’s 12V pin to the 12V power supply.
4. Plug the 12V power supply into a power source.
5. Wait for initialization process to complete.
The connection icon, located on the upper right of the screen, will turn green if connected.
*Note: If the connection icon does not turn green disconnect and reconnect power.
3.2 Software Operation
3.2.1 Settings Screen
The Settings Screen allows users to set the time and date, identify each optical sensor, update
serial numbers, and enable/disable sensors.
♦Users can manually set the date and time or choose to synchronize the C3 Submersible
Fluorometer to the PC date and time.
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♦Each channel (1-3) in the Settings Screen has a location associated with it on the C3
Submersible Fluorometer that is numerically labeled (1-3), respectively. Channels 4-6
are designated for the C6 Multi-Sensor Platform.
♦Click on the box adjacent to the channel to enable channel operation. If there is no
sensor installed users will be unable to select that channel.
♦Channels can be renamed using the dropdown selections or by manually entering a
name.
♦The serial number boxes are designed for the C6 Multi-Sensor Platform.
♦Settings will automatically be saved after exiting the Settings screen.
3.2.2 Current Data and Calibration Screen
The Current Data Screen allows users to view real-time data acquisition, in both tabular and
waveform formats, as well as conduct calibrations for each channel.
Current Data
Channel names are displayed but cannot be changed in the Current Data screen.♦
♦
♦
Real-time values are displayed next to each channel and in the adjacent Data Table.
A calibration button is available for each channel and the depth sensor.
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♦Real-time data can be saved by selecting the “Start Data Capture” button. Users will be
prompted to enter a file name and file location. Data files will be saved in (*.csv) format.
Tabular Screen
♦Real-time data including time, date, temperature, and units are continuously scrolling on
the tabular screen for enabled channels.
♦Channel names will appear in the associated column headings.
♦If units are not selected during calibration, a relative fluorescence units (RFU) label will
appear.
Waveform Screen Users can graphically view real-time data for each sensor by clicking the
“Display Waveform” box.
♦Channel names and units will be displayed on the Y-axis.
♦Time and date will be displayed on the X-axis.
♦Clicking the “Autoscale” box will automatically scale graphs.
♦Data can be saved during waveform mode by clicking “Start Data Capture”.
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Calibration Screen
Users can calibrate sensors in either the direct concentration mode, raw fluorescence mode,
or blank subtracted raw fluorescence mode.
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Direct Concentration Mode
Values reported in the Direct Concentration Mode are scaled to a predetermined standard
value and blank subtracted. The equation used to calculate concentrations after calibrating
to Direct Concentration Mode is:
Standard Value (units) x RFU Response = Concentration (units)
Standard RFU
Raw Fluorescence Mode Blank Subtracted
Values in the Raw Fluorescence Blank Subtracted Mode are noted as RFUB. It is important
to note that these values are blank subtracted but are not scaled to a standard; they are
relative values.
Raw Fluorescence Mode
Values in the Raw Fluorescence Mode are referred to as “Relative Fluorescence Units”
(RFU). It is important to note that these values are not blank subtracted or scaled to a
standard; they are relative values.
Direct Concentration Calibration
Following steps 1-5 will ensure values are reported as blank subtracted Concentrations in
units of choice. See Appendix B for recommended practices.
Step 1: Blanking
♦Place the C3 Submersible Fluorometer in a blank solution.
Note: A blank solution is a solution without the fluorophore of interest (i.e. de-ionized
water, artificial seawater, or filtered seawater)
Note: Ensure the Optical head is free of air bubbles
♦Wait until “Current RFU” readings have stabilized then select the “Set Blank” button to
set the blank value.
♦Future measurements for this sensor will be blank subtracted based on the blank
response recorded during calibration.
Step 2: Standard Value and Units
♦Place the C3 Submersible Fluorometer in a standard solution or use a secondary solid
standard (see Appendix D for more information on solid standards).
Note: Not all sensors are designed with solid standards
♦Enter the known concentration value of the standard solution in the “Standard Value”
box. If the concentration is not known, enter an arbitrary value (i.e. 100).
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♦Future measurements will be calculated based on the correlated response to the standard
value.
♦Enter manually or select desired units from the dropdown menu.
Note: Do not choose or enter “RFUB” if Direct Concentration Mode is used
Step 3: Set Standard
♦When readings in “Current RFU” box have stabilized, select the “Set Standard” button.
Step 4: Optional Temperature Compensation
Temperature compensation is optional and allows the user to automatically compensate to
the factory installed temperature sensor. Temperature compensation is available for
Chlorophyll aand Rhodamine sensors only. Temperature is displayed in degree Celsius.
♦Click on the “Temperature Compensation” box.
♦Select either the Chlorophyll aor Rhodamine from the dropdown menu.
♦Data will now be corrected for temperature fluctuations.
The temperature compensation coefficients for each fluorophore are listed in the table below.
Fluorophore Coefficient
Rhodamine 0.026 per degree C Exponential
Chlorophyll a
1.4% per degree C Linear
Step 5: Save Calibration
♦After calibration is complete, select “Save Calibration”.
♦Data for the selected sensor will now be calibrated.
Raw Fluorescence Calibration – Blank Subtracted
Following steps 1-5 will ensure values are reported as Blank subtracted Relative
Fluorescence Units (RFUB). See Appendix B for recommended practices.
Step 1: Blanking
♦Place the C3 Submersible Fluorometer in a blank solution.
Note: A blank solution is a solution without the fluorophore of interest (i.e. de-ionized
water, artificial seawater, or filtered seawater)
Note: Ensure the optical head is free of air bubbles
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♦Wait until “Current RFU” readings have stabilized then select the “Set Blank” button to
set the blank value.
♦Future measurements for this sensor will be blank subtracted based on the blank
response recorded during calibration.
Step 2: Selecting Units
♦Select RFUB from the units’ dropdown menu.
Note: Do not enter a value in the standard value box
Step 3: Skip and go to Step 4
Step 4: Optional Temperature Compensation – Follow same steps under the Direct
Calibration procedure
Step 5: Save Calibration
♦After calibration is complete select “Save Calibration”.
♦Data for the selected sensor will now be in relative fluorescence units and blank
subtracted.
Raw Fluorescence Calibration
In the Current Data screen select the “calibrate” button next to a specific channel. At the
bottom of the Calibration Screen, click to use “Uncalibrated Raw Fluorescence Mode”. Data
for that channel will be uncalibrated and reported as “Relative Fluorescence Units” (RFU).
Depth Calibration (Optional Accessory)
Depth is displayed in meters only. There are two calibration options for depth:
1. The first uses only the atmospheric pressure as an offset. This is suitable for any shallow
application, including most fresh water applications.
2. The second compensates for gravity variations with latitude, as designed from the
UNESCO Technical Papers in Marine Science #44. This method assumes 0°C and
35PSU salinity.
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Atmospheric Offset
Step 1 (Method 1):
♦Select the “Calibrate” button for depth in the “Current Data” screen.
♦Pressure in PSI will be displayed in the “Current Pressure” window.
♦After “Current Pressure” readings are stable at desired location select “Set Zero”.
Step 2 (Method 1):
♦Select “Atmospheric offset only”.
Step 3 (Method 1):
♦Select “Save Calibration” button.
♦Future depth values will be scaled to the offset.
Atmospheric and Gravity Offset
Step 1 (Method 2):
♦Select the “Calibrate” button for depth in the “Current Data” screen.
♦Pressure in PSI will be displayed in the “Current Pressure” window.
♦After “Current Pressure” readings are stable, at desired location, select “Set Zero”.
Step 2 (Method 2):
♦Select “Atmospheric and gravity offset”.
♦Enter the latitude.
Step 3 (Method 2):
♦Select “Save Calibration” button.
♦Future depth values will be scaled to the offset.
3.2.3 Log Setup Screen
The Log Setup screen allows the user to configure a logging session, activate the mechanical
wiper, and enable logging. C3 Submersible Fluorometer memory allows for a maximum of
480,000 data points.
Enter a log start and stop date (MM/DD/YYYY) and time (HH:MM:SS).
♦Enter the sampling interval (HH:MM:SS). The minimum sampling interval is 1 second.
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♦If the mechanical wiper is installed click the “Wiper” box to enable.
♦Select the number of revolutions from the dropdown box (1-10 revolutions). All sensors
will be wiped at specified revolutions before each measurement.
Note: If users select revolutions that exceed sampling interval a warning message will be
displayed
Note: Do not click the Wiper Box to enable wiper if the wiper is not installed
♦After log set up is complete select “Enable Datalog”.
♦A prompt will appear asking if user is ready to enable logging, select “Yes”.
Note: If data logging is set to start immediately, there will be a minimum delay of 100
seconds before startup after power has been supplied
WARNING! As soon as data logging is enabled users will be unable to conduct calibrations
or view current data. This should be the last step before the C3 Submersible Fluorometer is
de
p
lo
y
ed.
3.2.4 Downloading and File Management
Users can download new and exisiting files saved in the C3 Submersible Fluorometer
memory.
♦Select Download Data.
Note: This step may take up to 10 minutes depending on file size
♦When download has completed choose the files to be saved by clicking the “Save” box.
♦Users will be prompted to choose a folder location where data will be saved.
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Files will be saved in .csv format.
♦
♦
♦
Select “Clear Datalog” to erase existing data from memory.
Users are able to view data in the “Current Data” window if desired.
3.2.5 Integrating the C3 Submersible Fluorometer to a Third Party Platform
The C3 Submersible Fluorometer can be digitally integrated into a third party platform
including a CTD or datalogger.
After the instrument has been calibrated proceed to Log Setup (Section 3.2.3). After the
session has been initiated the C-Soft software will automatically shut down. Users should
communicate with the C3 Submersible Fluorometer via HyperTerminal serial terminal
emulator.
1. On an MS Windows computer, open the HyperTerminal program (Start→All
Programs→Accessories→Communications→HyperTerminal)
2. The Connection Description screen will appear. Name the connection description. This
file will save the communication parameters for the C3 Submersible Fluorometer and
can be used in the future to establish communication with the instrument quickly.
3. The Connect To screen will appear. Choose the appropriate communications port in the
Connect Using window. Click OK.
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4. The Port Settings screen will appear. Choose the following port settings;
Bits per second: 9600
Data bits: 8
Parity: None
Stop bits: 1
Flow control: Hardware
Click Apply and OK
5. Next, the HyperTerminal window will appear. You are now ready to connect the C3
Submersible Fluorometer to a power source. Once power is applied, the initial C3
Submersible Fluorometer screen will appear in the HyperTerminal window after 1 ½
minutes or at the predetermined log start time.
Most applications will integrate streaming data. Below are instructions on how to save
streaming data on a PC.
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To save data:
1. On the HyperTerminal window toolbar, choose Transfer and then Capture Text
2. When you click on Capture Text, a window will appear asking you to name and
save the .txt file to the location of interest.
3. Once you are finished, you will need to return to the HyperTerminal window
toolbar, choose Transfer and then Capture Text and select Stop. This will close
the .txt file.
4. Now open MS Excel or other data analysis software and open the .txt file that you created
in HyperTerminal. Choose ALL FILES from the file type field.
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4.0 Deployment & Accessories
4.1 Connecting the Submersible Battery Pack
The Battery Pack comes with a charger. There is also an optional 12-inch cable (P/N: 105-
2590) that is not needed if the optional battery bracket is installed. The battery is fully
charged after 8 hours.
♦After data logging is enabled attach the battery to the C3 Submersible Fluorometer with
the 12-inch cable or via battery bracket.
♦Secure C3 Submersible Fluorometer and battery to a fixed structure.
♦Data logging will begin at specified time and date.
Note: The battery will allow for over 85 days of logging at 15-minute intervals.
4.2 Battery Bracket Installation
The optional battery bracket was designed for easy self-contained compact deployment of
the C3 Submersible Fluorometer.
1. Align the stainless steel pin on the battery bracket with the associated pinhole on the C3
Submersible Fluorometer.
2. Apply pressure until the battery bracket is firmly attached the C3.
3. Thread the green plastic support line through the holes on the side of the bracket.
Green Line
4. The line should be flush with the ends of the support line holes on the bracket.
5. Slip the battery through the bracket and line up the 8-pin end of the battery with the port
on the C3.
6. Apply pressure until the battery is firmly attached to the C3.
7. An Allen wrench can be used to tighten the bracket at the end of the battery.
4.3 Installing the Mechanical Wiper
The C3 Submersible Fluorometer’s mechanical wiper is an optional accessory that
minimizes bio fouling during extended deployments. The wiper uses non-destructive brush
material to clean the optics allowing for accurate readings under extreme bio fouling
conditions. Users are able to select the number of wiper rotations before sampling.
Note: The wiper motor can not be retrofitted to a C3 Submersible Fluorometer. The wiper
motor must be ordered with instrument and factory installed at the time of purchase.
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