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SCUFA Submersible Fluorometer FAQ

What are the options for Internal Datalogging (IDL) configurations for the SCUFA and what is the total time available?

Please refer to the chart below:


Can I use Rhodamine WT as a secondary Standard for the SCUFA?

If you are using your SCUFA for in vivo chlorophyll readings, Turner Designs recommends that you use a Rhodamine WT standard of roughly 50-100ppb to simulate a signal.  You can also use the adjustable solid standard for the SCUFA that will produce a steady and repeatable signal.

I inherited a SCUFA, are instructions for the Flow Cap and specifications available?

The attached document provides information on connectivity requirements for the SCUFA Flow Cap.
View SCUFA Flow Cap Instructions

I lost the protective cover (aka dummy plug) for the data and power pins on my SCUFA, is this part still available?

The part number for the dummy plug is 002-0210. For pricing and availability please contact Turner Designs Accessory sales at 1-877-316-8049.  It is a good idea to use it at all times when the SCUFA is not connected to the interface cable.

How do I attach the SCUFA to a CTD?

Two pieces of hardware are required to integrate a SCUFA with a CTD - an integration cable and a mounting bracket.  If possible, the integration should be conducted by the CTD manufacturer.  If this is not possible, you must contact the appropriate cable/connector vendor to have an integration cable made that will allow communication between the fluorometer and CTD.  An integration cable consists of two in-line connectors, locking sleeves and a cable of specified length, usually 3-4 feet.

The in-line connector required for the SCUFA is an Impulse 8-pin, female connector (Impulse P/N: MIL-8-FS), the locking sleeve is P/N MCDLS/F.  The maximum cable length is 50m.

The bulkhead connector on the SCUFA is Impulse P/N:MCBH-8-MS.
The wiring for the SCUFA bulkhead connector is as follows:

1    V Batt +
2    V Batt –
3    RS-232 ground
4    RS-232 T1 Out
5    RS-232 R1 In
6    V Out 1
7    V Out 2
8    ground

What environmental factors cause error in in vivo chlorophyll analysis with the SCUFA?

Temperature has an inverse relationship with fluorescence.  In a vertical profile, as temperature decreases, the fluorescence will increase independent of chlorophyll concentration.  The SCUFA is equipped with temperature compensation to automatically correct data.  

Light history will have significant affects on the fluorescence in algal cells.  Cells will fluoresce more chlorophyll per cell when in darker environments than in well lit zones.  One way of reducing the effects of light is to use the flow-through cap when sampling natural waters.  By using a flow-through cap and an external pump, the algal cells will be dark-adapted before entering the fluorometer, significantly reducing fluorescence error caused by variations in the light history of the cells.
Dissolved organic matter (DOM), chlorophyll degradation products, and turbidity can also affect fluorescence response.  If these factors are suspected to be significant it is worth conducting a quick study to look at the effects by comparing the fluorescence from filtered and non-filtered water samples from below the photic zone where chlorophyll concentrations would be at a minimum.

Are there some steps I can take to troubleshoot my SCUFA?

The following are some common problems and solutions to diagnose your SCUFA:


Possible Cause

Possible Solution

The SCUFA will not communicate with SCUFAsoft program

The COM port may be in use by another program.

Check your PC setting to make sure that the correct COM port is selected. Check wiring between the PC and SCUFA to make sure that everything is connected correctly. Check to see that the SCUFA is powered.

The SCUFA will not power up.

The connector may not be fully seated

Check your connections to the SCUFA and refer to Appendix D of the manual.

The SCUFA is making erratic or incorrect readings.

This can be caused by an incorrect calibration.

To check calibration refer to page 11 of the SCUFA manual regarding recalibration.

The SCUFA has no Analog 0 to 5V DC output.

If the internal datalogging is activated there may be no Analog output.

Turn off internal logging.

The time and date on data is incorrect.

The PC clock may be incorrect

Reset your PC time and date. This is transferred from your PC while linked to the SCUFA.

The SCUFA will not detect low concentrations.

The optics on the SCUFA may be dirty.

Rinse the optics with fresh water and dry with Kim wipes or non-abrasive lens paper.

The Flow Cap on my SCUFA is leaking.

This can be caused by incorrect tubing or running at water pressure >10psi.

You should use 1/2" ID tubing when using a flow cap.

My chlorophyll extractive readings do not match my calculated values.

This can be caused by incorrect usage of standard and or calibration.

Match the solid standard and a known primary standard and recalibrate.

My Solid Secondary Standard readings keep changing.

This can be caused by dirty optics or your Solid Secondary Standard adjustment has changed

Verify the solid secondary standard as compared to a known standard and clean the optics

Data is not being collected by the IDL

This can be caused by not turning on data logging.

Make sure the IDL icon turns blue and is activated.

My SCUFA will not enter "sleep" mode after the IDL has been configured.

After you have configured the internal data logging screen in SCUFAsoft you must disconnect the serial cable and the power cable before the system will start using the IDL configuration.  Continuous Logging (24/7) or at least one daily record MUST be programmed before the IDL can activate.  Refer to page 17 of the SCUFA manual for more details on the IDL configuration.  If the serial cable is left connected to the PC the SCUFA will not power down.

What volume of liquid will the SCUFA Flowthrough Cap hold?

The SCUFA Flowthrough Cap will hold about 40mL of fluid.  If you are interested in finding a minimum sample volume, you must also include enough to account for tubing area.

Is the SCUFA's serial data temperature compensated?

If you purchased the temperature compensation package with your SCUFA, then as long as it is enabled (thermometer icon is active in SCUFA soft), the fluorescence output will be temperature compensated.  If the thermometer icon is not active then your readings will be uncompensated.

Can you provide an example of SCUFA Serial data output?

The following data set is an example of the RS232 serial data output captured by a serial data acquisition program. In this case, the Hyperterminal program that is included with the Windows operating system was used to save the data.  
Note:  The TCF item below stands for “Temp. Corrected Fluorescence” using a configurable Temperature Coefficient entered into the SCUFA.  In this case the coefficient value was set to zero, resulting in no correction.

Date            Time             Fluor         TCF         Turb         Temp
08/08/01     16:15:50:     18.898     18.898     83.289     26.3(C)
08/08/01     16:15:51:     18.896     18.896     83.673     26.2(C)
08/08/01     16:15:52:     18.980     18.980     82.341     26.2(C)
08/08/01     16:15:53:     18.950     18.950     80.537     25.7(C)
08/08/01     16:15:54:     18.947     18.947     80.523     25.0(C)
08/08/01     16:15:55:     18.952     18.952     80.525     24.4(C)
08/08/01     16:15:56:     18.949     18.949     80.525     23.8(C)
08/08/01     16:15:57:     18.939     18.939     80.516     23.3(C)
08/08/01     16:15:58:     18.945     18.945     80.521     23.1(C)
08/08/01     16:15:59:     18.951     18.951     80.525     22.8(C)
08/08/01     16:16:00:     18.944     18.944     80.527     22.7(C)

What is the range on the SCUFA solid secondary standard in Rhodamine WT equivalence?

The Solid Secondary Standard for the SCUFA is adjustable.  The solid standard contains a fluorescent material mounted on a threaded shaft that allows you to adjust the exposed rod section.  For Rhodamine use, the typical adjustable range would roughly simulate from 5ppb up to 80ppb of Rhodamine WT.

What is the sensitivity of the SCUFA?

The SCUFA sensitivity is defined in terms of the minimum detection limits of various analytes.
The SCUFA can detect:
Analyte               Minimum Detection Limit
Chlorophyll          0.02ppb or 0.02 μg/L
Rhodamine WT  0.04ppb or 0.04 μg/L
Turbidity               0.05NTU

Do I adjust the sensitivity with a gain knob or switch?

There is no manual sensitivity or gain control mechanisms on the SCUFA. There are three gain settings (x100, x10, x1) on the fluorescence channel and two gain settings on the turbidity channel that are controlled automatically.  With analog output, the user has control over instrument range that will affect the gain settings available.  For example, by setting the 0-5V range to 0-20ppb, you will eliminate the need for the x1 gain setting.  To achieve optimal performance, the appropriate calibration standard should be used.  An optimal standard will be a standard with a concentration that represents 40-60% of the maximum concentration you will experience in the field.

Is SCUFAsoft compatible with Macintosh computers?

No, SCUFAsoft is not compatible with Macintosh computers.

How often do I need to calibrate the SCUFA?

For greatest accuracy, check calibration before every deployment.  Verify the need to calibrate by reading a stable, known concentration standard, such as a solid secondary standard, immediately after calibration and again before each deployment to see if the readings have changed significantly.  Recalibrate when there is a change in the environment or when the accuracy becomes unacceptable for your study.

What is the purpose of the solid secondary standard?

The solid secondary standard is designed for recalibration in place of primary standards and to check for instrument performance and drift.  It is very stable and does not require special storage conditions.

What is the concentration of the solid secondary standard?

There is no exact concentration for the solid secondary standard. It is a relative concentration for both Chlorophyll and Rhodamine WT.  You can easily adjust the fluorescence signal of the solid standard and use it as a reference value for future calibrations as well as check for electronic drift.

What is the power consumption if using internal data logging?

When using internal data logging, the total power consumption is dependant on the sampling rate set by the user.  If the sampling rate is set to an interval longer than 1 reading every 5 seconds, the unit will power down into sleep mode (60mA).  The instrument will consume 60mA when logging data.

How long can the SCUFA stay submerged with anti-fouling screens?

The Copper Anti-fouling System is intended to be used for fluorometer deployments of extended periods (>1 day).  The copper components should be installed prior to instrument calibration.  The copper components will slowly dissolve in water and need to be monitored for wear.  It is recommended that all components be changed after two months of use.

How do I set the 0-5V outputs?

Setting the 5V to a value greater than the 0V activates analog calibration for the channel of interest - fluorescence and/or turbidity.  When analog output is activated, the Internal Data Logging (IDL), if purchased, is automatically disabled and the IDL screen will be faded out.
Activating the analog signal output should follow instrument calibration.  By calibrating first, you can then set the 0V and 5V to calibrated values.  For example, if you calibrated with a 10ppb solution and know that you will not exceed 100ppb in the field, you can set 5V to equal 100.  By doing this you can optimize the resolution and accuracy of your analog data and interpret your analog data with a calibration coefficient.  In this example, the calibration coefficient would be 20 (5V = 100ppb, 0.5V = 10ppb).
Once set, the analog output will be activated upon the next power up as long as the unit is not connected to the portable computer.

What is the Flowthrough cap for?

The Flowthrough cap is an optional accessory that can allow the SCUFA to be used in a Flowthrough mode.  The cap is installed over the optics and has inlet and outlet ports to connect with a plumbing system.  A common use of the cap is in conjunction with Sea-Bird CTD systems that can use a submersible pump to pump water through all of the probes.  Another use could be to use the cap on a ship or in the lab with an external pump.  The cap is not necessary for use.  The SCUFA has been designed as an open-optics unit, meaning it can operate successfully with high levels of ambient light without the need for a pump.

How can I use the SCUFA in the laboratory?

There are two ways that the SCUFA could be used to analyze samples in the laboratory.  The optical head of the SCUFA could be immersed into sample solution. The SCUFA should be held at least 2" off the bottom of the container.  The second option is to use the Flowthrough cap with an external pump or syringe.

How does the SCUFA detect and quantitate chlorophyll in water?

Chlorophyll naturally absorbs blue light and emits red light.  The SCUFA will detect chlorophyll by transmitting an excitation beam of light in the 440nm (blue) range and by detecting the light emitted by the sample in the 680nm (red) range.

What is in vivo chlorophyll analysis?

In vivo chlorophyll analysis is the fluorescent detection of chlorophyll in living algal and cyanobacteria cells in water.  In this technique, the excitation light from the fluorometer passes through the untreated sample water and excites chlorophyll within the living cells of the algae present.  Due to the nature of light, cells and other dissolved and particulate materials in the water will affect the excitation light before it reaches the chlorophyll molecules.  Examples of interfering materials include other plant pigments and degradation products, dissolved organic matter, turbidity, and cell morphologies.  Therefore, in vivo analysis is a semi-quantitative tool. In vivo numbers should correlate well with each other but rarely can they be used as actual chlorophyll a concentration measurements until correlated with extracted chlorophyll a data.

Could I calibrate with extracted chlorophyll?

No. Methanol, 90% acetone and other organic solvents will react with the SCUFA's delrin housing.  The SCUFA should not be used to measure extracted chlorophyll. Please use a separate fluorometer such as the Turner Designs 10-AU or Trilogy Fluorometers to determine actual chlorophyll concentrations.

What variables will effect the linearity of a sample?

Fluorescence intensity is typically directly proportional (linear) to concentration.  When a concentration is too high, light cannot pass through the sample to cause excitation; thus very high concentrations can have very low fluorescence (concentration quenching).  The fluorometer reading rises at a decreasing rate and eventually begins to decrease, even though the concentration is still increasing.  Diluting a sample 1:1 or some other convenient ratio may check linearity.  If it is linear, the reading will decrease in direct proportion to the dilution.

How does photochemical decay affect fluorescence?

Many fluorescent molecules can be bleached or destroyed by light (fading of dyes in the sun).  Ultraviolet light, especially, can cause certain molecules to break down. Fluorescence readings decrease as the molecules are destroyed.  Rate of destruction varies depending upon environmental factors, temperature. Fluorescein, for example, is destroyed rapidly in sunlight. Rhodamine WT, however, is adequately stable for field studies.  For chlorophyll measurements, samples and standards need to be kept in the dark until read.  All flow measurements should employ opaque delivery hoses to minimize photochemical interference.

What are the advantages of fluorescence?

Sensitivity:  Limits of detection depend to a large extent on the properties of the sample being measured.  Detectability to parts per billion or even parts per trillion is common for most analytes.  Fluorometers achieve 1,000 to 500,000 times better limits of detection as compared to spectrophotometers.

Specificity:  Spectrophotometers merely absorb light.  Spectrophotometric techniques are prone to interference problems because many materials absorb light, making it difficult to isolate the targeted analyte in a complex matrix.  Fluorometers are highly specific and less susceptible to interferences because fewer materials absorb and also emit light (fluoresce).  And, if non-target compounds do absorb and emit light, it is rare that they will emit the same wavelength of light as target compounds.

Simplicity and Speed:  Fluorometry is a relatively simple analytical technique.  Fluorometry's sensivity and specificity reduce or eliminate the sample preparation procedures often required to concentrate analytes or remove interferences from samples prior to analysis.  This reduction in or elimination of sample preparation time not only simplifies, but also expedites the analysis.

Is there any maintenance that you recommend for the SCUFA?

We suggest that you rinse the SCUFA off with fresh water after every deployment, and that you inspect the cables and connectors for signs of wear. You should clean the optics and calibrate as often as needed for your application. ****Note the seals and O-Rings are designed to last indefinitely. No maintenance is required on these parts.