Turner Designs C3 User manual

User’s Manual
December 5, 2018
P/N: 998-2300
Revision S
TURNER DESIGNS
1995 N. 1st Street
San Jose, CA 95112
Phone: [phone]
FAX: [phone]

C3 and C6P Submersible Fluorometer
Table of Contents
1.
Introduction
1.1
Introduction
4
1.2
Important Note Regarding the Use of Fluorescein Optics
4
2.
Inspection and Setup
2.1
Instrument Checklist
5
2.2
Optional Accessories
6
2.3
Identification
8
3.
C-Soft Windows™ User Interface
3.1
Software Installation and PC Requirements
9
3.1.1
Minimum PC Requirements
9
3.1.2
Software Installation
9
3.1.3
Integration / Interface Adapter Cable Installation
10
3.1.4
PC Software Interface
10
3.2
Software Operation
11
3.2.1
Settings Screen
11
3.2.2
Current Data and Calibration Screen
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
22
4.1.1
Rinsing
22
4.1.2
Care for the Bulkhead Connector
22
4.2
Warranty Terms
22
4.3
Warranty Service
23
4.4
Out of Warranty Service
23
Appendices
A
Specifications
25
B
Recommended Practices
26
C
Wiring Guide
27
D
Linear Range, Quenching and Temperature Considerations
28
E
How to set up HyperTerminal for Digital (ASCII) Data Capture
29
F
Integrator Firmware
31
G
Campbell Scientific CR1000 Datalogger Integration
32

C3 and C6P Submersible Fluorometer
WASTE ELECTRICAL AND ELECTRONIC EQUIPMENT (WEEE) DIRECTIVE
Turner Designs is in the business of designing and selling products that benefit the
well-being of our environment. Accordingly, we are concerned with preserving the
surroundings wherever our instruments are used and happy to work with customers
by complying with the WEEE Directive to reduce the environmental impact resulting
from the use of our products.
WEEE Return Process:
To arrange the return of an end-of-life product, proceed as follows:
If you purchased your instrument through a Turner Designs Distributor please
contact your local representative. They will instruct you where to return the end-
of-life product.
If you purchased your instrument directly from Turner Designs please contact
Turner Designs Customer Service
By Phone: [phone] or Toll Free: [phone]
By Email: Customer Service at [e-mail]
Turner Designs will provide a WEEE RMA Number, a Shipping Account
Number, and a Ship to Address. Package and ship the product back to Turner
Designs.
The product will be dealt with per Turner Designs’ end-of-life recycling program in
an environmentally friendly way.

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998-2300 Rev. S Page 4
1. Introduction
1.1 The C3 and C6P Submersible Fluorometers are manufactured according to users’
optical specifications with one, two, three, four, five or six optical sensors ranging
in wavelengths from deep ultraviolet to infrared. Each optical sensor is designed
with fixed excitation and emission filters. The C3 and C6P Submersible
Fluorometers come 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 and C6P 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 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]
This does not apply to the C6P Submersible Fluorometer.

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2. Inspection and Setup
2.1 Instrument Checklist
The C3 P/N: 2300-000 and C6P P/N: 2360-000 Submersible Fluorometer package
includes:
C3 or C6P Submersible Fluorometers
Factory-installed temperature sensor
Antifouling Copper Tape - C3 only P/N 2300-506.
Interface cable for communicating with your PC and supplying power to the
instrument P/N 2200-150
Integration / Interface Adapter Cable (see Appendix F and G for more
information about integration) P/N 2300-115
USB Flash Drive including C-Soft software, user’s manual, cable guide and
quick start guide
Temperature SensorTemperature Sensor
12V Power Supply12V Power Supply
Computer Interface Cable
Integration / Interface Adapter CableIntegration / Interface Adapter Cable
Antifouling Copper TapeAntifouling Copper Tape

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2.2 Optional Accessories
Pressure sensor P/N 2300-360 Factory-installed. Note: Can only be
installed during the manufacturing of the unit.
Copper 3-Arm Mechanical Wiper P/N 2300/2360-450 Factory-installed. Note:
Can only be installed during the manufacturing of the unit.See Accessory
Instructions on the USB Flash Drive for more information.
Copper Wiper Arm Kit P/N 2300-459/2360-459
Replacement Wiper Brushes P/N 2300-460
Replacement Wiper Spacers P/N 2300-462
Antifouling Copper Tape P/N 2300-506 –available only for the C3.
Antifouling Copper Plate P/N 2300/2360-507
Rechargeable Submersible Battery Pack including charger P/N: 2200-601.
See Accessory Instructions on the USB Flash Drive for more information.
Battery Bracket P/N 2300/2360-603 Note: Required for use with Battery
Pack and C3 Analog Output Adaptor.See Accessory Instructions on the
USB Flash Drive for more information
High Capacity Submersible Battery with Charger and Cable P/N 3200-600.
See Accessory Instructions on the USB Flash Drive for more information.
Flow Cap P/N 2300/2360-700.See Accessory Instructions on the USB Flash
Drive for more information.
Shade Cap P/N 2300/2360-500 or C-ray Shade Cap P/N 2300-502.
Note: We recommend use of the shade cap as it provides a fixed
distance for calibration and sample measurement and minimizes effects
from ambient light.
Shade Cap Weight P/N 2300/2360-510
C-ray Towed Deployment Body P/N 2300-750 –available only for the C3.
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 P/N 2200-170
Solid Secondary Standard Cap P/N 2300/2360-905

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Solid Secondary Standard (SSS) for in vivo Chlorophyll, Phycocyanin,
Phycoerythrin, Rhodamine, and Fluorescein P/N 2300-901. See Accessory
Instructions on the USB Flash Drive for more information.
Solid Secondary Standard (SSS) for UV Sensors - CDOM/FDOM, Optical
Brighteners, Refined Fuels and Crude Oil P/N 2300-902. See Accessory
Instructions on the USB Flash Drive for more information.
Note: Solid Secondary Standard not available for turbidity.
Analog Output Adapter P/N 2300-480 - available only for the C3.See
Accessory Instructions on the USB Flash Drive for more information.
Flow CapFlow Cap
Booster Kit
Battery BracketBattery Bracket
C-ray Towed Deployment BodyC-ray Towed Deployment Body
Submersible BatterySubmersible Battery
Solid Secondary Standard Cap
Solid Secondary Standard
Solid Secondary Standard Cap
Solid Secondary Standard
Shade Cap
Air Purge Slots
Shade Cap
Air Purge Slots
High Capacity Submersible Battery
with Charger and Cable
Copper 3-Arm Mechanical Wiper

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2.3 Identification
Sensors are marked with numbers located adjacent to the optics on the face of the
C3 and C6P Submersible Fluorometers. These numbers correspond to channels
1 through 6 in C-Soft (C3 and C6P software). Note: Channel names can be
modified using C-Soft.
Light emitting diode color table.
Application
Light Source Color
In Vivo Chlorophyll
Blue
Red
Turbidity
Infra Red (No Color)
Phycocyanin
Yellow-Orange
Phycoerythrin
Green
Fluorescein
Blue
(See important note on page 5)
Rhodamine
Green
CDOM/FDOM
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)*
Tryptophan
Deep 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 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 USB Flash Drive (also located on the Turner Designs
Software / Firmware webpage under Customer Care).
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 the "C-Soft" icon is located on the desktop.
C-Soft Note: You may receive a warning message asking if you
want to unblock messages, select "Unblock".
Note: For Windows 10 users, the operating system may install C-
Soft on the Compatibility mode. You can correct this by right
clicking on the C-Soft icon and selecting properties.
If you are having
problems with C-Soft in
Windows 10 uncheck
the compatibility box.

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3.1.3 Integration / Interface Adapter Cable Installation
1. Insert the USB Flash Drive and install the Adapter Cable driver
(Integration-Interface_Adapter_Drivers.exe) onto your PC.
2. Make sure nothing is plugged into the Adapter Cable’s connectors.
3. Plug the USB connector into a USB port on your computer and wait for
hardware to automatically install.
4. Once USB is installed and ready to use, right click the My Computer
Icon. Note: For Windows Vista or 7 users, open the start menu
and right click on Computer.
5. Left click “properties” to open the properties window.
6. If running Windows XP or older versions of Windows, click on the
“Hardware” tab and then click “Device Manager” to open the list of
devices installed on your computer. Note: For Windows Vista or 7
users, the Device Manager link is located in the upper left part of
the properties window; you will not see a Hardware tab.
7. Scroll down and open the “Ports” heading from the list.
8. The newly installed Adapter will be titled “USB Serial Port” followed by
a COM port designation in parentheses (for example, “(COM 5)”).
9. If the USB Serial Port’s COM designation is labeled as any number
from 1-6, your installation is complete. Close all windows and make
sure to set C-Soft to that specified COM designation when trying to
connect via USB Adapter Cable connection.
10. If the USB Serial Port’s COM designation is greater than 6, right click
on the “USB Serial Port” and click “properties” which will open up the
properties menu. From that menu click on the “Port Setting” tab and
then click “Advanced” which will open the advanced settings menu for
that USB Serial Port. Choose any COM port 1-6 from the COM port
pull-down menu and click “OK”. Note: Ideally you want to start with
any port that is not in use; if all are in use then choose any port 1-
6. Click “OK” to the warning box if it appears and Click “OK” to close
any other open menus. Your installation is complete. Make sure to set
C-Soft to that specified COM designation when trying to connect via
USB Adapter Cable connection.
3.1.4 PC Software Interface
Note: It is important that the steps be followed IN ORDER. Any
variance from the procedure may result in the connection NOT being
established.
1. Plug either the USB or serial connector of the adapter cable into your
computer.
Note: Either connection can be used for communicating and
configuring the instrument.

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2. Plug the interface cable onto the 8-pin bulkhead connector of the
instrument.
3. Plug the interface cable’s serial plug into the adapter cable’s male serial
plug.
4. Begin C-Soft by double-clicking on the C-Soft icon and choose the
appropriate COM port from the pull down COM menu.
5. Plug the 12V power supply into a power source.
6. 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 and C6P Submersible Fluorometers to the PC date and time.
Each channel (1-6) in the Settings Screen has a location associated
with it on the C3 and C6P Submersible Fluorometers that is numerically
labeled (1-6), respectively. Channels 4-6 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 and C6P.

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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, and view calibration information.
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 Submersible Fluorometer in a blank solution.
Note: A blank solution is a solution without the fluorophore of
interest (i.e. deionized 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: Standard Value and Units
Place the Submersible Fluorometer in a standard solution or use a solid
secondary standard. See Accessory Instructions on the USB Flash
Drive for additional information.
Note: Turbidity sensors do not have solid secondary 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 Submersible
Fluorometer to compensate for changes in fluorescence due to varying
temperatures as detected by the temperature sensor. Temperature
compensation is available for in vivo Chlorophyll and Rhodamine sensors
only. Temperature is displayed in degree Celsius.
Click on the “Temperature Compensation” box.
Select either in vivo Chlorophyll or Rhodamine from the dropdown
menu.

C3 and C6P Submersible Fluorometer
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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 / °C Exponential
in vivo Chlorophyll
0.014 / °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 Submersible Fluorometer in a blank solution.
Note: A blank solution is a solution without the fluorophore of
interest (i.e. deionized 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)
Note: Make sure your instrument is calibrated for depth and there is a
value set even if you do not have a depth sensor.
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
http://unesdoc.unesco.org/images/0005/000598/059832EB.pdf. This
method assumes 0 °C and 35PSU salinity.
Atmospheric Offset (Method 1)
Step 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:
Select “Atmospheric offset only”.
Step 3:
Select “Save Calibration” button.
Depth values will now be scaled to the offset selected.

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Atmospheric and Gravity Offset (Method 2)
Step 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:
Select “Atmospheric and gravity offset”.
Enter the latitude.
Step 3:
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 and C6P
Submersible Fluorometer can log over 60,000 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.

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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” (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 a time in the past, 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 Submersible Fluorometer in
order to log data, capture real-time data output, and/or integrate with other
instrumentation (see Appendix F and G for more information about integration).
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 and C6P Submersible
Fluorometer is deployed.

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Note: Use the Battery Life Calculator available on the Turner Designs
website C3 and C6P product pages 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. Low battery can result in
intermittent logging.
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. Note: Check the optical face when power is supplied to make sure
the sensors light. The sensor will turn on, then off and then turn back on in
100 seconds. If this sequence does not happen, cycle power.
3.6 Downloading and File Management
Users can download new and existing files saved in the Submersible Fluorometers
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.