Limiting the Size and Duration of Data Files: autoexec.bat

When preparing for a long duration deployment it is important to consider the length of the data file that will be generated. MicroRiders are often deployed for days or weeks at a time. The default setting on RSI instruments is to collect a single data file unlimited in size. A file collected over days or weeks can be unmanageable in post processing. Furthermore, a file can be lost if the instrument is turned off incorrectly while recording. To limit the size and duration of resulting data files use the flag -t followed by the number of records you would like in each file (1 record is approximately 1 second) . Please note that you will loose 30 to 40 seconds of data every time a file is written; users often use 3600 records (approximately 1 hour). To change your system to automatically use the command odas5ir -f setup.cfg -l 3000 -t 3600 you will need to change the autoexec.bat file:

1. Download the file to your data acquisition computer,
2. Edit the contents of the file to be odas5ir -f setup.cfg -l 3000 -t 3600, or the number of records you prefer,
3. Delete the existing autoexec.bat off the CF card,
4. Upload the new autoexec.bat file to the CF card.

Please note the flag -l 3000 sets the clock on the instrument. For instruments with the Tidal Energy Configuration, which use a sample rate of 1024Hz, the clock must be set to -l 6000.

Warning: Commands on the autoexec.bat file are case sensitive.

To learn more about PicoDOS commands, please review the ODAS5-IR User Guide available in our downloads section.

Canada’s first three-glider mission maps whale habitat

Ocean Tracking Network:

For the first time in Canada, a triple glider project has successfully mapped out critical gray whale habitat off the west coast of Vancouver Island. While previous missions have deployed one or two gliders, this Whales, Habitat, and Listening (WHaLe) project—funded by the Marine Environmental Observation, Prediction, and Response (MEOPAR)—is the first to fly three coordinated gliders.

In addition to the common suite of water property sensors—temperature, salinity and oxygen—the gliders on this mission carried a broadband hydrophone to identify and count whale vocalizations, an echo sounder to remotely quantify zooplankton biomass variability, and optical instrumentation identifying phytoplankton to elucidate the major components of the whale food chain. The University of British Columbia glider also carried a specialized Rockland Scientific sensor suite for measuring ocean turbulence, to better understand why submarine canyons create such favourable habitat for the whales.

Continue Reading…

The 1st Summer School of Upper Ocean Turbulence, Gdańsk 2016

The purpose of the ‘Summer School of Upper Ocean Turbulence’ was to teach students (graduate students and scientists) in the art of turbulence theory, processes and measurements with the focus on the upper ocean.

The 2 week course included a 2 week intensive training period (25 July – 5 August) with lectures by a diverse set of international experts that intend to cover a broad spectrum of problems ranging from application of spectral methods in turbulence data analysis to numerical methods in turbulence research. The last week of the program (8-12 August) included at sea data collection and hands-on experience in data analysis with VMP250 turbulence microstructure profiler. Read More>>

OMG 2017: Ocean Microstructure Glider Training

Ocean Microstructure Glider training, “OMG 2017”, is a 4-day training workshop that covers all aspects of turbulence measurements using MicroRider integration with ocean glider platforms. The training workshop will cover setup, operation, maintenance, deployment and processing of turbulence data. The workshop is scheduled for April 24-27, 2017 in Victoria, B.C. Canada. Please see the OMG 2017 Preliminary Schedule for details. The event promises to bring together a diverse group of scientists from around the world. Seats are limited, to register please fill out the OMG 2017 Registration Form.


How to Make a Hotel File

MicroRider mounted on an ocean glider

In order to process data from a velocity shear probe the speed of the instrument or flow over the probes must be obtained. When using a Vertical Microstructure Profiler (VMP) the pressure data can be used to determine speed. However, pressure data cannot be used to obtain speed when profiling horizontally with a MicroRider. In most cases, speed must be determined by using an secondary source such as an acoustic doppler velocimeter, an electromagnetic flow sensor or speed records from an AUV or glider.

If your RSI instrument is mounted on a vehicle that provides mission files, you may wish to integrate the data provided in the mission file into your data processing. In some cases the data recorded by the vehicle is required to process the p-file. There are currently four scripts and functions in the ODAS MATLAB Library for extracting information out of mission files and placing it into a hotel file.

The hotel file is ingested by odas_p2mat and interpolated on to the time vector t_slow in your p-file. The resulting data vectors are saved to the same mat-file as the data vectors produced from the p-files. The most common use of a hotel file is to import speed data from a vehicle when the RSI instrument is not able to measure the speed itself (such as an AUV equipped with a MicroRider, or a Seaglider equipped with MicroPods). An accurate speed estimate is required to convert shear probe data into physical units and to compute gradients of temperature and conductivity. Other data of interest measured by the controller in a vehicle include CT data, pressure, pitch, roll and heading, for example.

If you would like to processes your data without a hotel file, please indicate a reasonable constant speed in meters per second. For example: odas_p2mat(‘file_name.P’,’constant_speed’,1.2)

For more information and an example of Hotel File setup, please review Section 10 of Technical Note 39. Please login or register on our website to download this technical note.

Please join us 2017 April 24-27

If you are interested in learning more about Hotel Files, please join us for our annual Ocean Microstructure Glider training (OMG 2017), scheduled for 2017 April 24-27 .

Scientists Explain How Meltwater Reaches Ocean Depths

January 30th, 2017 Press Release 
An international team of researchers has discovered why fresh water, melted from Antarctic ice sheets, is often detected below the surface of the ocean, rather than rising to the top above denser seawater. The team found that the Earth’s rotation influences the way meltwater behaves – keeping it at depths of several hundred metres.

The research is published this week in the journal Nature in association with colleagues at University of Southampton, National Oceanography Centre, Southampton, University of East Anglia (UEA), British Antarctic Survey (BAS) and Stockholm University. Read Full Article

Live LAMTOV demo at Ocean Business 2017

Rockland Scientific and OceansScan-MST are pleased to announce our free live demo of the LAMTOV (Light Autonomous Microstructure Turbulence Vehicle) at Ocean Business 2017. The LAMTOV is an integration of Rockland’s neutrally buoyant MicroRider 1000 and OceanScan-MST’s LAUV. Please join us to experience this exciting collaboration.

The dockside demonstration will begin at 10:30 on Wednesday, April 5th with a follow-up classroom session at 12:00 on Thursday, April 6th.

To register for the free demo please follow the link here.

Rockland Scientific’s neutrally Buoyant MicroRider 1000







Video of the Light Autonomous Underwater Vehicle from OceanScan-MST

Happy Holidays: Office closed from December 26-30

Please be advised that the Rockland Scientific office will be closed between December 26th to the 30th 2016. Everyone at Rockland wishes you a joyous holiday season especially if you find yourself at sea during this time.

If you require support over the holidays please do not hesitate to contact We will respond promptly to any inquiries.

Happy Holidays from everyone at Rockland Scientific International


Instrument Communication Troubleshooting

While operating a Rockland Scientific Microstructure Instrument you may experience difficulty with instrument communication. Here are some troubleshooting tips to help ensure reliable communication with your internally recording instrument.

In order to communicate, you will need your microstructure instrument, the instrument deck cable and a computer. You will need to connect to your computer via a USB port as well as a 9-pin RS-232 D-sub serial port. If you do not have a serial port on your computer you can use a RS-232 serial to usb adaptor cable. Not all adaptor cables are equal, so if you find one that works well for you then hang on to it!

9-pin RS-232 D-sub serial port

9-pin RS-232 D-sub serial port

RS-232 Serial to USB Adaptor

RS-232 Serial to USB Adaptor

Required Software

There is usually no need to install any software on the Persistor computer in your instrument because this will be done at RSI before the instrument is shipped. However, you must install two programs on your computer. One is Motocross, which provides terminal emulation and serial communication with the instrument and permits the transfer of files, including executable software files. The other is RSI-link, a USB link utility that permits the bi-directional transfer of files between your computer and the instrument. All registered users can download Motocross and RSI-Link as part of a file called ODAS5-IR from the downloads section of our website. To register please fill out the required information under “Register”. You must make an account and receive authorization before downloading.

ODAS5-IR and ODAS5-IR User Manual in Downloads Section

ODAS5-IR and ODAS5-IR User Manual in Downloads Section

Mac vs PC

We recommend using a PC rather than a Mac computer. There are some work-arounds if you must use a Mac. The Motocross Terminal Emulator will not work on Mac computers so we recommend CoolTerm as a replacement for Motocross on Mac computers. CoolTerm allows for reliable communication and file transfers, however it will not allow you to reformat the CF card. For a complete work-around we recommend installing VirtualBox on your Mac and running Windows7.

Which version of windows is preferred?

The following versions of windows are supported: WindowsXP, Windows7, Windows8, Windows8.1, Windows10.

COM Port Number

Motocross has difficulty communicating with serial COM Ports that are not between 1 and 10. If you are having difficulty communicating please check your the serial COM port number and change if necessary. You can access COM ports by opening your Device Manager in the Control Panel while connected to your instrument.

USB 3.0 vs USB 2.0

We are currently experiencing difficulties with instrument communications through USB 3.0. Please use the USB 2.0 port on your computer whenever possible. If you do not have a USB 2.0 port you can use a USB 3.0 to USB 2.0 adaptor cable or hub.

Still having Communication trouble?

Please review your instrument manual and the ODAS5-IR manual or contact us if you would like more information regarding instrument communications.



Winches Optimized for Turbulence Profilers

When choosing a winch for your turbulence profiler it is important to consider the deployment characteristics of turbulence profilers. Unlike a CTD Rosette, turbulence profilers descend in what is known as tethered free-fall. Tethered free-falling is when a profiler is allowed to fall uninterrupted and decoupled from the vessel and/or ocean surface motions. To achieve this, the tether must be coiled on the surface of the water by hand so that the profiler can take up the slack as it falls.

Tethered free-fall. Note the slack in the orange tether.

Tethered free-fall. Note the slack in the orange tether.

While there are many options available, it is important to find a winch that works well for your turbulence profiler. Some important considerations include the following:

Free wheeling is an important capability of winches optimized for turbulence profilers. Free wheeling is enabled by the addition of  clutch that can be disengaged. Free wheeling the winch allows for a single operator to pull line or cable off the winch. For shorter profiles it may be practical to mark the line at the depth desired, take that much line off the winch and form a coil on the deck before deploying the profiler. For longer profiles it is best to work with a partner; one person pulling line off the winch in free wheel mode and the other casting the line into the water.

PID-02 Winch with microCTD Turbulence Profiler aboard the R/V John Strickland

PID-02 Winch with microCTD Turbulence Profiler aboard the R/V John Strickland

Recovery of turbulence profilers is the most important function of a winch. In many cases it is impractical to recover the profiler by hand. Recovery by winch can speed up the process allowing for more profiles to be taken during a cruise. When using a real time instrument please remember to use a sheave that accommodates the bend radius of the telemetry cable. Automatic level winders are also a useful feature. If an automatic  level winder is not included a boat hook can be used to guide the cable/line back onto the winch.    

Real Time and Internally Recording Turbulence Profilers have different winch requirements. Real time profilers require a telemetry cable as well as a slip-ring to allow data to be transferred from the cable on the rotating winch drum to a deck cable and finally to a computer. Winches for internally recording profilers do not require a slip-ring and generally require a lower pull strength because they do not need to lift the heavy cable. Winches optimized for internally recording profilers are often smaller such as the PID-02 which can be lifted easily by two people and secured to the deck of smaller vessels.    

Rockland Scientific partners with A.G.O. Environmental to provide a wide range of winches. A.G.O.’s team recently joined the Rockland crew for a field trip as part of the VicTOR 2016 training week. You can read more about the field trip here:  A.G.O. Field Trip with Rockland Scientific