Water column sampling using Sea-Bird CTD

Sea-bird product line is vast and divers, in this post we will only teach how to use Sea-Bird SBE19plus V2 in profile mode without a deck unit (Ship communication system), although many parts of this post will also apply to other instruments and to sampling while using a deck unit.
This post was written in order to help people when sampling alone and is very detailed to achieve its purpose.
External links are highlighted in yellow text.
Establish communication
Due to backward compatibility issues, Sea-Bird devices use RS-232 communication protocol. Such devices are using Serial port (Image 1, A) for communication with the PC. Although serial ports were the norm in personal computers for years, many modern computers are not equipped with such ports, to overcome this problem, we now use serial to USB converters (Image 1, B).  Since communication problems are common when sampling with a CTD, we highly recommend that if you are purchasing a computer to be used for CTD sampling, you will acquire one that has a serial port.

Image 1: A - Serial port. B - Serial to USB converter.

The converters comes in many sizes and shapes, but they all require installing a driver software. Usually the driver can be downloaded from the manufacturer website, or you can use a CD supplied with the device.

After installing, plug in the serial to USB converter in one of your USB sockets, a virtual serial port is created. First, make sure that this port was created and find out the port number using "device manager":

To open the device manger software, open your file windows file manger manager and right click on "This computer">properties>device manager. After opening the device manager, go to "Ports", expand the list of ports and identify you serial port (remember the number in brackets after the name). Since the naming varies with adapters and windows versions, you can use the screencast or have a look at image 2 to identify the converter's port number.

Image 2: Windows device manager

Software

Seabird has a suite of software called SeaSoft which you can download from the company website. This suit includes the three programs that are usually used when sampling with a CTD:

SeaSave - This software is used to acquire CTD data to disk and display it in real time. It can also display archived data. When using a deck unit, this software controls the operation of the rosette. Its important to mention that the way SeaSoft programs look and behave is extremely configurable and is controlled using .psa (program setup files) and .dsa (display setup file) files.
SeaTerm - This program is used for programming the CTD and for downloading data saved on the device.
SBEdataconversion - This program is used when post processing the data acquired when sampling. In a separate post we describe the data conversion process we usually perform.

Before sampling, its essential to know three types of files:

1. psa - program settings file
2. dsa - display settings file
3. xmlcon - instrument configuration

For further info regarding those file read the designated post here.
Before sampling with the CTD, preferably before you exit the office, make sure everything works:

• Connect the communication cable to the PC (using the adapter if needed).
• Check the connection by performing a dummy sampling:
• Switch on the CTD using the magnetic switch.
• Go to Real time data>start and then push the button to select output data file name (select a file that you can easily identify as test run)
• make sure you use the correct instrument configuration file (its a good idea to use a date in the file name)
• Push the start button and see that communication is established (otherwise, use the troubleshooting post here).
• Make sure that all the sensor are responding and produce sensible readings.
• Blow into the pump to check the salinity, Temperature and Oxygen sensors that are connected to the pump.
• Use your hand to cover optical sensors and see that they respond.
• Exit SeaSave and switch off the CTD using the magnetic switch.

When arriving to a sampling station perform the actual sampling:

• Connect the communication cable to the PC (using the adapter if needed).
• Check the connection before you put your device in the water:
• Switch on the CTD using the magnetic switch.



• Go to Real time data>start and then push the button to select output data file name. Its important to define a file name that is meaningful, the following lines I assume using the MichSave script we use for naming CTD files.



• Run the MichSave script by double clicking it
• Select the project number from the list
• Write the sampling station name
• SeaSave will be launched automatically, push the "select output data file name" and paste (CTRL+V). This will paste the automatically generated file name.
• Select the "Begin archiving data when ‘Start Archiving’ command is sent" option
• Make sure you are using the correct instrument configuration file (its a good idea to use a date in the file name).
• Click start
• Wait for communication
• Lower the instrument into the water (preferably to a. 5m depth).
• Wait for the instrument readings to stabilize.
• Lift the instrument back to the surface
• Click real time data>start archiving
• Sample your profile
• Make sure you are not lowering your device faster than 1m s$^{-1}$
• Closely observe your readings while sampling!
• When done sampling close the sampling by clicking real time data>stop