Turner Designs C3 User manual

User’s Manual
September 19, 2011
P/N: 998-2300
Revision H
TURNER DESIGNS
845 W. Maude Ave.
Sunnyvale, CA 94085
Phone: [phone]
FAX: [phone]

C3 Submersible Fluorometer
Table of Contents
1. Introduction
1.1 Introduction 4
1.2 Optical Sensors 4
1.3 Important Note Regarding the Use of the Fluorescein Sensor 5
2. Inspection and Setup
2.1 Instrument Checklist 6
2.2 Optional Accessories 7
2.3 Identification 9
3. C-Soft Windows™ User Interface
3.1 Software Installation and PC Requirements 10
3.1.1 Minimum PC Requirements 10
3.1.2 Software Installation 10
3.1.3 PC Software Interface 10
3.2 Software Operation 11
3.2.1 Settings Screen 11
3.2.2 Current Data and Calibration Screens 12
3.3 Calibration Procedures
3.3.1 Direct Concentration Calibration 15
3.3.2 Raw Fluorescence Calibration – Blank Subtracted 16
3.3.3 Raw Fluorescence Calibration 17
3.3.4 Depth Calibration (Optional Accessory) 17
3.4 Log Setup Screen 18
3.5 Enabling Data Output Ready State 19
3.6 Downloading and File Management 20
4 Maintenance and Warranty
4.1 Maintenance 21
4.1.1 Rinsing 21
4.1.2 Care for the Bulkhead Connector 21
4.2 Warranty Terms 21
4.3 Warranty Service 22
4.4 Out of Warranty Service 22
Appendices
A C3 Submersible Fluorometer Specifications 24
B C3 Submersible Fluorometer Recommended Practices 25
C C3 Submersible Fluorometer Wiring and Cable Guide 26
D Linear Range, Quenching and Temperature Considerations 28
E C-FINS Installation Guide 29
F Installing the Battery Bracket 33
G Connecting the Submersible Battery Pack 34
H Installing the Mechanical Wiper 35
I Installing the Flow Cap 36
J Using the Secondary Solid Standard 38
K C-Series Analog Adapter 40
L How to set up Hyperterminal for Digital (ASCII) Data Capture 43

C3 Submersible Fluorometer
Equipment Specified as Electrical and Electronic Waste

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1. Introduction
1.1 The C3 Submersible Fluorometer is manufactured according to users’ optical
specifications with one, two, or three optical sensors ranging in wavelengths
from deep ultraviolet to infrared. Each optical sensor is designed with fixed
excitation and emission filters. 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 to minimize
biofouling. The C3 Submersible Fluorometer Windowsbased user interface
allows for easy calibration of each sensor, digital data reporting, data logging
and digital or analog export of data.
1.2 Optical configurations for Turner Designs’ standard applications:
Application Minimum
Detection Limit Dynamic Range Excitation Emission
In Vivo Chlorophyll a0.025 µg/L 0-500 µg/L 430 nm 685/50 nm
Phycoerythrin
(Marine Cyanobacteria) 150 cells/ml 0-150,000 cells/ml 540 nm 575/10 nm
Phycocyanin
(Freshwater Cyanobacteria) 150 cells/ml 0-150,000 cells/ml 595 nm > 645 nm
CDOM 0.4 ppb QS* 0-2500 ppb QS* 350 nm 430/30 nm
Turbidity 0.05 NTU 0-3000 NTU 850 nm 850 nm
Crude Oil 0.2 ppb PTSA** 0-2700 ppb PTSA** 350 nm 410-600 nm
Refined Fuels 2 ppb NS*** 0-10,000 ppb NS*** 260 nm 300-400 nm
Optical Brighteners 0.6 ppb PTSA** 0-15,000 ppb PTSA** 350 nm 445/15 nm
Fluorescein Dye
(See important note below) 0.01 ppb 0-500 ppb 485 nm 540 nm
Rhodamine Dye 0.01 ppb 0-1000 ppb 550 nm > 570 nm
PTSA Dye 0.01 ppb 0-650 ppb 365 nm 405/10 nm
* Quinine Sulfate in 0.05 Molar H2SO4
** 1,3,6,8-Pyrenetetrasulfonic Acid Tetrasodium Salt
*** 1,5-Napthalene Disulfonic Disodium Salt
Custom optical configurations are available on request.

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1.3 Important Note Regarding Use of Fluorescein Optics:
For C3’s manufactured prior to 2/15/2011, the Fluorescein sensor should
not be enabled for simultaneous data collection with Chlorophyll and/or
Rhodamine sensors or it will produce unreliable results. For C3’s
manufactured after 2/15/2011 this interference issue was corrected. If you
would like to send your C3 back to Turner Designs to resolve this
interference issue, please contact [email protected]

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2. 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 communicating with your PC and supplying power to the
instrument
♦CD including C-Soft software, user’s manual, and quick start guide
Temperature SensorTemperature Sensor
12V Power Supply12V Power Supply
Computer Interface Cable

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Submersible BatterySubmersible Battery
2.2 Optional Accessories
♦Pressure sensor (P/N: 2300-360) Factory-installed (Note: Can only be
installed during the manufacturing of the unit.)
♦C3 Mechanical Wiper (P/N: 2300-450) Factory-installed (Note: Can only be
installed during the manufacturing of the unit.)
♦Replacement Wiper Brushes (P/N: 2300-460)
♦Replacement Wiper Spacers (P/N: 2300-462)
♦Rechargeable Submersible Battery Pack including charger (P/N: 2200-601)
♦Battery Bracket (P/N: 2300-603) (Note: Required for use with Battery
Pack and Analog Output Adaptor.)
♦Flow Cap (P/N: 2300-700)
♦Shade Cap (P/N: 2300-500) or C-ray Shade Cap (P/N 2300-502)
♦ Shade Cap Weight (P/N: 2300-510)
♦C-ray Towed Deployment Body (P/N 2300-750)
♦Extender Cables:
♦10 meters (P/N: 105-2595)
♦25 meters (P/N: 105-2596)
♦50 meters (P/N: 105-2597)
♦Custom lengths available upon request
♦Booster Kit (P/N: 2200-900) (Note: Required for cable lengths greater
than 10 meters.)
♦24” Pigtail Interface Cable with Locking Sleeve (2200-170)
♦24” Integration Cable (P/N: 2200-160) or 5m Integration Cable (P/N: 2200-
165) (Note: Used for continuous data output and communication with
the C3, NOT intended for uploading firmware to the C3.)
♦Secondary solid standard (P/N: 2300-900) for multiple sensors (Note: Not
available for turbidity or ultraviolet sensors.)
♦C-Series Analog Output Adapter (P/N: 2300-480)
Mechanical WiperMechanical Wiper

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Booster Kit
Battery BracketBattery Bracket
Shade Cap
Air Purge Slots
Shade Cap
Air Purge Slots
Flow CapFlow Cap
Secondary Solid Standard
Solid Standard Insert
Secondary Solid Standard
Solid Standard Insert
Computer Integration Cable
yellow heat shrink
Computer Integration Cable
yellow heat shrink
C-ray Towed Deployment BodyC-ray Towed Deployment Body

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2.3 Identification
Sensors are marked with numbers 1, 2, or 3 located adjacent to the optics on
the face of the C3 Submersible Fluorometer. These numbers correspond to
channels 1, 2, and 3 in C-Soft (C3 software). Note: Channel names can be
modified using C-Soft.
Light emitting diode color table.
Application Light Source Color
Chlorophyll aBlue
Turbidity Infra Red (No Color)
Phycocyanin Yellow-Orange
Phycoerythrin Green
Fluorescein Blue
(See important note on page 5)
Rhodamine Green
CDOM Ultra Violet (No Color)*
Refined Oils and Fuels Deep Ultra Violet (No Color)*
Crude Oil Ultra Violet (No Color)*
Optical Brighteners Ultra Violet (No Color)*
PTSA Ultra Violet (No Color)*
*Do not look directly at the optics. Ultraviolet light can be damaging to the eyes.

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3. C-Soft Windows™ User Interface
The C-Soft Windowsbased user interface allows for intuitive calibration, data
logging, set up, and download functions.
3.1 Software Requirements and PC Installation
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 website on
the Support page).
3. Open the C-Soft software folder and double click on the setup icon.
4. The software will automatically be installed in the PC’s (C:/Program
Files/C-Soft) folder unless user selects alternate location.
5. 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. http://www.belkin.com/
search for Part Number: F5U409v1
2. Connect the 8-pin female end of the interface cable to the C3
Submersible Fluorometer’s 8-pin male connector.
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.

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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.
♦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 and are disabled for the C3.
♦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. There is no serial number associated with the sensors in
the C3.
♦Settings will automatically be saved after exiting the Settings screen.

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3.2.2 Current Data and Calibration Screen
The Current Data Screen allows users to view real-time data acquisition,
in both tabular or waveform display, 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.
♦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 as .csv format.
Tabular Screen
♦Real-time data including date, time, units and temperature 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.

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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. Users
may also rescale graphs by unchecking the “Autoscale” box and
manually entering desired values for either Y or X axis ranges.
♦Data can be saved during waveform mode by clicking “Start Data
Capture”. Data files will be saved as .csv format.

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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.
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:
Raw Fluorescence Blank Subtracted Mode
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.
Standard Value (units)
Standard RFU x Sample RFU = Concentration (units)
Standard Value (units)
Standard RFU x Sample RFU = Concentration (units)

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3.3 Calibration Procedure
3.3.1 Direct Concentration Calibration
Following steps 1-5 below 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 and
ensure the optical head is free from air bubbles.
Note: A blank solution is a solution without the fluorophore of
interest (i.e. de-ionized water, artificial water, or filtered water).
♦Wait until “Current RFU” readings have stabilized then select the “Set
Blank” button to set the blank value.
♦Wait for the blank value to be measured and set for all 3 gains.
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: UV and Turbidity sensors cannot be used with solid
standards.
♦Enter the known concentration value of the standard solution or solid
standard in the “Standard Value” box. If the concentration is not
known, enter an arbitrary value.
♦Enter manually or select desired units from the dropdown menu.
Note: Do not choose or enter “RFUB” if Direct Concentration
Mode is preferred.
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; it enables the C3 to compensate
for changes in fluorescence due to varying temperatures as detected by
the C3’s 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 Chlorophyll aor Rhodamine from the dropdown menu.
♦Data will now be corrected for temperature fluctuations.

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The temperature compensation coefficients for each fluorophore are
listed in the table below.
Fluorophore Coefficient
Rhodamine 0.026 / °C Exponential
Chlorophyll a0.014 / °C Linear
Step 5: Save Calibration
♦After calibration is complete, select “Save Calibration”.
♦Data are now displayed as concentration estimates.
3.3.2 Raw Fluorescence Calibration – Blank Subtracted
Following steps 1-5 below 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 water, or filtered water).
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.
♦Wait for the blank value to be measured and set for all 3 gains.
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
as the Direct Concentration Calibration procedure in Section 3.3.1.
Step 5: Save Calibration
♦After calibration is complete select “Save Calibration”.
♦Data are now displayed as blank corrected relative fluorescence
units.

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3.3.3 Raw Fluorescence Calibration
In the Current Data screen select the “calibrate” button next to a specific
channel. At the bottom of the Calibration Screen select, “click to use
Uncalibrated Raw Fluorescence Mode”. Data for that channel will be
uncalibrated and reported as “Relative Fluorescence Units” (RFU).
3.3.4 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 also compensates for gravity variations with latitude, as
designated from the UNESCO Technical Papers in Marine Science
#44. This method assumes 0 °C and 35PSU salinity.
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.
♦Depth values will now be scaled to the offset selected.

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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.
♦Depth values will now be scaled to the offset selected.
3.4 Log Setup Screen
The Log Setup screen allows the user to configure a logging session, set the
mechanical wiper to its home position, and enable logging. The C3
Submersible Fluorometer can log just over 64,000 lines of data.
Enter a log start date (MM/DD/YYYY) and time (HH:MM:SS).
♦ Enter the sampling interval (HH:MM:SS). The minimum sampling interval is
1 second.
♦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.

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♦After log set up is complete select “Enable Datalog” (see section 3.3
“Enabling Data Output Ready State).
♦A prompt will appear asking if user is ready to enable logging, select “Yes”.
Note: If data logging is set to start for some past time, there will be a
minimum delay of 100 seconds before startup after power has been
supplied. Otherwise wait until the data logging start time has been
reached for data logging to begin.
3.5 Enabling Data Output Ready State
The Data Output Ready State must be enabled for the C3 Submersible
Fluorometer in order to log data, capture real-time data output, and/or integrate
the C3 with other instrumentation. There are five necessary steps to ensure the
instrument is properly set up for data output:
1. Set the instrument’s clock to PC or local time in the Settings Tab.
2. Select the sensors you expect to use during sampling.
3. Calibrate selected sensors for either Direct Concentration Mode or Raw
Fluorescence Units Blanked (RFUB) Mode (see section 3.3).
4. Set the start time, sampling, and wiping intervals in the Log Setup Tab.
Note: wiping interval is optional and depends on the sampling interval
(see section 3.4).
5. Click the ‘Enable Datalog’ button followed by the ‘Yes’ button to enable the
Data Output Ready State.
WARNING! As soon as data logging is enabled users will be unable to access C
-
Soft settings. This should be the last step before the C3 Submersible Fluorometer
is deployed.

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Note: Use the Battery Life Calculator available on the Turner Designs
website C3 product page to calculate a conservative estimation of how
many days you can expect to log data. Factors such as battery charge
and water temperature will affect logging days.
A few seconds after the ‘Yes’ button has been clicked to enable the Data Output
Ready State, the C-Soft program will automatically shut down and users must
disconnect power and serial connections. The instrument is now in the Data
Output Ready State and will remain in that state so long as C-Soft is not used to
communicate with the instrument. Note: As soon as C-Soft is used to
communicate with the instrument, users will need to re-set the parameter
settings in the Log Setup (section 3.4) and again enable datalog to put the
instrument into the Data Output Ready State.
When power is supplied to the instrument while it is in the Data Output Ready
State, it will begin streaming data after a 100 second delay. If power is cycled
(i.e. disconnected and reconnected) please allow 100 seconds for the data
stream to begin.
3.6 Downloading and File Management
Users can download new and existing 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.
♦ Files will be saved in .csv format.
♦ Select “Clear Datalog” to erase existing data from memory.
♦ Users are able to graphically view downloaded .csv data files using C-Soft
software if desired.