Ocean Instruments SoundTrap ST500 User manual

SoundTrap ST500 User Guide
May 2019

1 About this guide ..............................................................................................................................4
2 Quick start guide .............................................................................................................................5
2.1 Opening and closing the housing.....................................................................................5
2.2 Batteries...........................................................................................................................5
2.3 Installing the hydrophone................................................................................................6
2.4 Install the SoundTrap host on your PC.............................................................................6
2.5 Connect SoundTrap to your PC........................................................................................7
2.6 Check SoundTrap Status ..................................................................................................8
2.7 Configure the deployment...............................................................................................8
2.8 Begin recording using the IR Remote Control................................................................10
2.9 Data Offload...................................................................................................................11
3 More details ..................................................................................................................................12
3.1 Adding additional memory cards...................................................................................12
3.2 Data Files........................................................................................................................13
3.3 Calculation of deployment endurance...........................................................................14
3.4 Deployment hardware ...................................................................................................15
3.5 Software updates...........................................................................................................16
3.6 MSP firmware updates...................................................................................................16
3.7 Calibration......................................................................................................................16
3.8 Troubleshooting.............................................................................................................19
4 Appendices....................................................................................................................................20
4.1 SoundTrap HF Click Detector (ST500HF Only)................................................................20

4.1.1 Click detector..........................................................................................................20
4.1.2 Snippet extractor....................................................................................................21
4.1.3 User parameters.....................................................................................................21
4.1.4 Output File formats ................................................................................................22
4.1.5 Click Detector Caveats and Cautions......................................................................24

1About this guide
This guide begins with a ‘Quick start’ section to help you get going with your new SoundTrap, including
software installation and basic deployment instructions. This is followed by several sections containing
more detailed information around operation, deployment, maintenance and troubleshooting. It is
highly recommended you read the entire guide to ensure you have a good understanding of the
instrument and how to get the most from its capabilities.

2Quick start guide
2.1 Opening and closing the housing
Before opening the housing always check for flooding by shaking the recorder and listening for water
sloshing around inside. If flooding is suspected, then be aware that the housing may be pressurised
and therefore potentially dangerous. Carefully relieve any pressure by opening the small seal screw
at the base of the housing.
Opening the housing:
•Find the ‘open this end’ sticker on the housing.
•Screw open the endcap by turning counter clockwise
•You will probably need to insert a lever arm (eg screwdriver) in the provided holes to gain
sufficient leverage.
Closing the housing:
•Carefully check the O’rings. Any nicks or scratches indicate they must be replaced.
•Lubricate O’rings with silicone grease.
•Check O’rings are properly seated and absolutely free of stray hair/grit etc
•Insert the chassis in the housing and screw all the way home, using a lever arm if necessary.
•Difficulty in screwing home the cap may indicate insufficient o’ring lubrication; do not apply
excessive force –instead correct by applying o’ring lubricant.
•Replacement O’Rings should be type 78x3 N70 (Nitrile)
The O’ring checks are critically important to avoid damage. Any detritus or damage to the O’rings
may result in the housing being flooded which will almost certainly destroy the electronics.
2.2 Batteries

The SoundTrap ST500 is powered by up to 9 ‘D’cell alkaline batteries. These are loaded in sets of 3,
meaning the recorder can be deployed with 3, 6 or 9 batteries depending on desired length of
deployment.
We strongly recommend only using Energizer batteries. These are commonly available and all
testing and advertised battery endurances have been based on this brand. Performance of other
brands is unknown. Most importantly, Energizers are guaranteed not to leak electrolyte when left in
a discharged state. Other battery brands may leak, potentially causing damage to the electronics.
Where possible we recommend checking the voltage of each cell with a multi-meter, prior to
inserting into the recorder. Checking each cell will avoid the possibility of a bad (low voltage) cell. A
single bad cell can significantly affect the recorder endurance and potentially cause damage through
leaking electrolyte. Each cell should have a voltage of at least 1.5V.
Be careful to ensure correct battery polarity as indicated by the diagram in the battery
compartment. Once loaded, double check each battery’s polarity. Just one reversed battery is
enough to severely impact the overall battery life, and potentially cause damage through leaking
electrolyte. Always double check each cell’s polarity.
It is then very important that you verify the supply of power to the electronics. To do this press the
‘BAT’ button on the IR remote and observe the SoundTrap’s red status LED. If all is well you should
see two long red flashes. Note that there is a 10 second delay between connecting the batteries and
the software determining that the supply is stable. Observation of the two long flashes is
confirmation that at least one set of batteries are correctly installed and ready to go.
A single short red flash indicates a problem. In this event, inspect the batteries for correct insertion
and adequate battery condition.
2.3 Installing the hydrophone
From the factory you’ll find the (removable) hydrophone stored inside the battery compartment for
shipping. Unpack and plug it into the wet socket in the recorder endcap, then secure with the locking
collar. The hydrophone is the most fragile component of the system, so best remove it during
transport, and take care to avoid impacts or crushing during deployment.
2.4 Install the SoundTrap host on your PC
To start using your SoundTrap you’ll need to install the SoundTrap Host software.

For correct operation of your ST500 it is critical to use SoundTrap Host version 3.3.1 or
later.
•Pre-installation Notes:
oThe SoundTrap host software supports Windows 7,8 & 10 (32 or 64 bit versions).
oDo not connect the SoundTrap to your computer until you have completed the
SoundTrap host software installation.
oThe installation will be smoother if you’re logged into windows as an administrator.
•Visit www.OceanInstruments.co.nz/downloads/ to download the software.
•Download and run the installer.
•Once the install completes, run the SoundTrap Host application.
2.5 Connect SoundTrap to your PC
•Connect the SoundTrap using the USB cable provided.
•The drivers will take a couple of minutes to install. Once complete you should see your
SoundTrap appear in the ‘Device List’ on the left, as shown in figure 1.
•Select your SoundTrap by clicking its label on the left.
Figure 1 - The Device List

2.6 Check SoundTrap Status
Note the ‘Status’ panel on the right (Figure 3). Verify that the memory is not full.
Figure 2 –Deploy Control
2.7 Configure the deployment
•Select the ‘Deploy’ tab as shown in figure 2.
•Configure the deployment parameters as follows:
oThe ‘Recording Starts’ section determines when recording will begin. Recording can
begin immediately on disconnection of the USB cable, at a pre-determined date and
time, or manually using the IR remote control. Note that the remote can always be
used to override the other options.
oThe ‘Recording Schedule’ section provides selection of continuous or periodic
recording. For continuous recording simply leave the ‘Periodic Recording’ option
unchecked.

oOptions available in the ‘Audio Options’ will vary according to your device’s
capabilities. Options include the following:
▪Channel Selection selects which channels to record on.
▪Sample Rate should be set based on the frequency band of interest and
data rate considerations. A 96 kHz sampling rate is often a good choice for
general environmental noise measurements. Contact OI support if unsure.
oDetector –see HF Click Detector section below.
•Once you’ve made your selections click the deploy button which will save the settings and
you’re ready to go. The instruments internal clock is synchronised to your PC when you click
the deploy button. If you change your mind about something, just re-select the instrument
from the ‘Device List’.

2.8 Begin recording using the IR Remote Control
You may use the remote control to start recording. The
recorder housing must be open to receive the signal from the
remote.
•Press ‘START’ to start recording.
•Press ‘STOP’ to stop recording.
•If you have set a recording to start recording at a
later time, the recorder will blink red to indicate it
is ‘armed’ and waiting.
•The ‘armed’ state is cancelled by pressing Stop key.
•Re-enable the armed state by pressing the ARM
button.
•You can verify recording has started by checking for slow blinking of the status (green)
indicator.

2.9 Data Offload
Once you’re done recording, reconnect your SoundTrap to your PC and select the Retrieve Tab, as
shown in figure 4.
Figure 3 –Retrieve Tab
•You will see a list of files in the SoundTrap’s memory, including the file name (made from the
device serial number plus local date and time), date recorded, approximate size and whether
it has yet been downloaded to your computer’s hard drive.
•Download individual files by right clicking the file and selecting ‘download’.
•By default, all files will be downloaded to a ‘SoundTrap’ folder under My Documents. This
default location can be changed under the ‘Tools’ menu.
•Click the ‘Open Save Folder’ button to open the download folder location.
•To download all files, select all files using the shift key, then click the ‘Download’ button.
•To delete, click the ‘Delete All’ button. Files cannot be deleted individually.

•For faster download in the field, or to save disk space, un-check the ‘Decompress’ checkbox.
This will disable the decompression step of the offload process, meaning you will end up
with ‘sud‘ files only. These can be decompressed into wav files at a later time using the ‘File
Extraction’ option under the tools menu.
3More details
3.1 Adding additional memory cards
The SoundTrap ST500 series have the capacity to add additional data storage in the form of 3
microSD card slots. Two reasons to consider using these are:
1. To lengthen deployment endurance by adding more memory. When using a high sample
rate, the internal memory may get exhausted before the batteries are depleted. Adding
memory cards may extend the recording duration by up to four times.
2. To enable quick field servicing. The internal memory is non-removable, meaning the data
must be downloaded by USB which can take several hours. Using memory cards enables fast
retrieval of data ie a fast re-deploy can be achieved by simply swapping out the memory
cards and batteries.
Important things to note before using addition memory:
1. You should only use the recommended memory cards –Samsung Evo MicroSD. Counterfeits
of these cards are common, so only source from reputable suppliers. Using other card types
or counterfeits may result in performance issues such as greatly increased power
consumption, sampling gaps or unreliable recording.
2. The cards are used in the sequence 3->2->1->0 where 0 is the internal memory and 3 is the
bottom-most external card. Any full or missing cards will be skipped.
3. It is critical that each card is formatted prior to each deployment. This can only be done in
the SoundTrap recorder using the ‘Delete All Files’ option. This must be done for each card
individually.

4. SoundTrap uses a custom file system to maximise performance and reliability. This means
the cards can only be read with the ‘SoundTrap Card Reader’ application supplied with the
SoundTrap Host software. When inserting the memory cards into a PC you may receive a
message like “Drive is not formatted, do you want to format it now?”. Agreeing to this will
result in loss of data. Instead select ‘No thanks’ and run the SoundTrap card reader
software.
3.2 Data Files
Downloads produce several types of files:
o‘sud’ files which are the raw downloaded file. This is a compressed file and therefore
ideal for storing or sending of complete recordings. It can then be decompressed at
a later time into the following constituent file formats.
o‘wav’ files containing the audio. This is a Microsoft WAV format file that can be
opened by any media player, matlab, raven etc.
o‘xml’ files which contain metadata such as date recorded, gain setting, etc.
o‘csv’ files containing ancillary sensor data (e.g. temperature)
All file types follow the same naming convention consisting of the device serial number followed by
the date and time of the start of the recording in the format YYMMDDHHMMSS.
For duty cycled recording there will usually be one file per recording period. For continuous
recording a maximum file length of 1036800000 samples (2GB of wav) will determine the length of
the files. This equates to 1 hour recordings for a 288khz sample rate.
Where smaller than 2G files are desired for continuous recording it is recommended to set a duty
cycle with ‘zero off time’. For example, a duty cycle of 30 minutes every 30 minutes will result in
continuous 30 minutes files with no missing samples between files.

3.3 Calculation of deployment endurance
An excel spreadsheet is provided on the website to help with the calculation of deployment times
for differing deployment parameters. The spreadsheet provides deployment estimates, as well as
identifying one of three possible deployment constraints: battery capacity, memory capacity, or file
count. While the first two are obvious, the file count constraint requires explanation.
The file system used by SoundTrap currently has a minimum file size of 4 MB. When using periodic
recording, if the programmed ‘record for a period of’ period is very short, the resultant file may be
smaller than the minimum file size. This will result in inefficient usage of memory, and the
deployment may be artificially memory limited. For example, a SoundTrap ST500 has 256 GB of
memory; dividing this by the minimum file size of 4 MB gives a maximum of 64000 files.
This limitation becomes an issue when using low sample rates in combination with X3 compression.
By experimenting with the periodic recording parameters in the deployment spreadsheet it will
become clear how to best avoid this limitation.

3.4 Deployment hardware
The anchoring scheme used is very dependent on the goals of the data collection in combination
with the deployment environment. Thankfully SoundTraps are more easily deployed than traditional
acoustic recorders due to their small size. A SoundTrap ST500’s weight in water is approximately 1.5
kg.
Most often the hydrophone is located near the sea floor, using an anchored line. This involves
running a line between a heavy anchor weight and either a surface or sub-surface float. A sub-
surface float is often best, as it is less affected by weather/swell and is less likely to be tampered
with. The SoundTrap should be attached to the line a couple of meters off the bottom. Two grooves
at the top and bottom of the housing provide attachment points for cable ties for this purpose. The
cable ties should be threaded through the associated holes so they cannot slip off.
Be mindful that a taut line combined with strong currents may result in ‘cable strum’ which may
disrupt your recordings. In this case a rigid frame may be more appropriate.

3.5 Software updates
New software releases will be made available via the Ocean Instruments website. You may which to
subscribe to our email list in order to receive notification of these updates. The update procedure is
generally straightforward –simply install the new software over top of the existing, by running the
msi file and following the usual Windows software install prompts.
The software updates will typically include updates to both the windows software as well as the
device firmware. The updating of the device firmware is an automatic process that occurs when
pressing the ‘deploy’ button.
3.6 MSP firmware updates
From time to time a software release may include an update to the ‘MSP’ firmware. This is a special
section of the device firmware that changes infrequently. In the rare event that an MSP update is
required, the user will be advised during the deploy procedure and will be asked to connect the
‘reset battery’. This is a security feature that ensures the MSP firmware cannot be unintentionally
modified. In the case of the ST500 the reset battery is replaced with a (somewhat hidden) reset
switch. This is located just above the top memory card slot. To press it you will need something long
and pointy, such as a small screw driver. The switch is operated by pressing toward the circuit
board.
When asked to ‘connect the reset battery’ you must hold down the reset switch. Once the switch is
held down you can click the OK button (may require second person!) as per the software
instructions. You will then be asked to remove the reset battery (release the button). This done, the
MSP firmware update will proceed and complete within a few seconds. If presented with the error
message “MSP Erase failed”, it is likely that the pressing of the reset button was interrupted –please
try again.
3.7 Calibration
Two calibrations are associated with each ST500 system –the for the recorder, and that for the
hydrophone.
Recorder Calibration
Each ST500 recorder is factory calibrated to determine the electronic gain of the system. This
calibration process consists of inputting a tone of known signal level (in volts) and observing the

signal level recorded. The calibration data is provided as an end-to-end value. This represents the
rms voltage that will result in a normalised (±1.0) wav file with a full scale signal ie 2.0 units peak-
peak.
A typical value is -1.8 dB re 1 V.
Hydrophone Calibration
Each SoundTrap hydrophone is factory calibrated. The standard factory calibration consists of a
piston phone calibration at 250 Hz. This is expressed as dB re 1V / uPa.
A typical value is 177.0 dB re. 1 μPa/V.
End-to-end System Calibration
To determine the end-to-end (overall) system calibration simply add the recorder and hydrophone
calibrations together. Eg -1.8 dB + 177.0 dB = 175.2 dB re 1 uPa.
Obtaining the calibration values
Calibration data is not shipped with the recorder, but instead made available online from the
calibration page of the Ocean Instruments website. To find the values for your recorder and
hydrophone simply enter their serial numbers into the website here:
http://www.oceaninstruments.co.nz/
The hydrophone serial number is usually printed on both the hydrophone bulb and the wet
connector collar. The recorder serial number can be found in the SoundTrap Host software.
Applying the calibration
Application of the calibration data varies depending on the software used. Descriptions follow for
some of the most commonly used software.
MATLAB
To convert wav data to units of uPa, simply scale by the end-to-end calibration value. Example code:
[y, Fs] = wavread(filename) ; % read wav data from file
cal = 173.3; % value from calibration sheet
cal = power (10, cal / 20); % convert calibration from dB into ratio
y = y * cal; % multiply wav data by calibration to convert to units of uPa

PAMGUARD
PAMGAURD expects calibration data in terms of gain and ADC range. To work around this, specify a
preamplifier gain of the calibration value * -1.0 (eg -176.0) and specify the Peak-Peak voltage range
as 2.0 V.
PAMGuide
PAMGuide provides several convenient calibration schemes. For SoundTrap data select the end-to-
end calibration type and enter a system sensitivity of the calibration value * -1.0 (eg -176.0).
Audacity
Audacity reports SPL in units of dB re full scale. To scale SoundTrap data use the following:
Value in dB re 1 uPa = audacity value + end-to-end calibration –3dB;
For example, if the end-to-end value from the calibration sheet is 176.0 dB, and audacity reports a
level of -70 dB, the calibrated SPL is 103.0 dB re 1 uPa.

3.8 Troubleshooting
First port of call when experiencing problems is to check that you are using the most up to date
software. Oftentimes small issues are most easily resolved by updating the software –please try this
first. The latest software can be downloaded from here:
www.OceanInstruments.co.nz/downloads/
Problem: SoundTrap doesn’t appear in device list when plugged into computer
Solution: This is usually due to the internal lithium battery being dead flat. When deploying for long
periods the battery may become discharged to the point the device is incapable of communicating
over the USB. Quickest solution is to:
1. Disconnect the SoundTrap from the USB
2. Close the SoundTrap Host software
3. Reconnect the SoundTrap to the USB
4. If the blue LED indicator does not light, press the STOP button on the remote
5. The blue LED indicator should now light to indicate battery is charging.
6. Leave for at least 30 minutes to allow the battery to recover.
7. Start the host software and confirm device connects.
Problem: SoundTrap still won’t connect despite having recharged the batteries.
Solution: In cases of extreme battery discharge (e.g. a SoundTrap that has been in storage for
several months), it may be necessary to reset the device hardware. Before doing the reset, first
ensure you have recharged the battery as above. Then perform a hardware reset:
1. Disconnect the SoundTrap from the computer USB port.
2. Momentarily press the rest button located next to the top memory card slot.
3. You should see the green LED blink to indicate a successful reset.
4. Connect the SoundTrap to the USB.
8. Start the host software and confirm device connects.

4Appendices
4.1 SoundTrap HF Click Detector (ST500HF Only)
The SoundTrap ‘HF Click’ Detector is a general purpose high frequency click detector followed by a
snippet extractor. The detector is designed to detect most odontocetes and is intended to be used
as a first pass, guiding you to times in your recordings with lots of transients. You would typically use
the detector with a low detection threshold so that it makes a lot of false detects but also detects
most genuine clicks (i.e., high sensitivity, low specificity). You then evaluate the reported detections
in Pamguard to reduce obvious false detects, to classify clicks into species groups, and to identify
bouts, as you would with a continuous wideband recording. The benefits of doing on-board click
detection are that you get much longer recording times from your SoundTrap and you can identify
times of interest more quickly when you get the data back. The downside of course is that you do
not have the full wideband recording on the SoundTrap. This is mitigated in SoundTrap’s detector by
recording a short snippet of wideband sound around each detection. A few 100's of µs is often all
that is needed to classify odontocete clicks into general classes. The detector can be configured to
also make a continuous recording at lower bandwidth that allows you to quantify the general
ambient noise conditions, an important factor affecting detector performance, as well as the
presence of low frequency whistles that can help with species identification.
4.1.1 Click detector
The click detector comprises an approximate pre-whitening filter followed by a power-in-band
Constant False Alarm Rate (CFAR) detector. The whitening filter (a 35kHz high-pass filter) corrects
the typical low-frequency emphasis of underwater ambient noise creating a more spectrally-
balanced signal for the detector. The power-in-band detector consists of a highpass Finite Impulse
Response (FIR) filter (approximate 3 dB bandwidth 115 - 160 kHz) followed by a moving average
power estimator. The duration of the moving average window is a user parameter (see below). In
parallel, the power of the full bandwidth whitened signal is measured using a much longer
exponential window to give an estimate of the ambient noise power. This is used to adjust the
absolute detection threshold: a detection will be made if the power-in-band is greater than the
ambient power by more than the Relative Detection Threshold (RDT) which is a user parameter.
When a detection is made, the time of the detection and the ambient noise power at the time are
passed to the snippet extractor. A user-selectable blanking time must then elapse before another