The Octopus of Saanich

By Jackson Chu and Danielle Ludeman

As part of the Oceans Network Canada observatory, the Victoria Experimental Network Under the Sea (VENUS) provides real-time measurements, images, and sound to researchers and observers on-shore.

Anyone, from scientists to the general public, can access the network’s data and monitor environmental changes as they happen (see here for a previous post on accessing and graphing VENUS using R). The VENUS instrumentation is found in the coastal waters of the Salish Sea and is the sister network to the offshore NEPTUNE Canada regional cabled ocean network

Video and data provided by Jackson Chu

Captured in this time-lapse video from Saanich Inlet is a juvenile, ~10 cm long, Pacific Red Octopus (Octopus rubescens), which had temporarily moved underneath the VENUS Camera Array for a month. When the oxygen levels drop to near zero, it decides to pack up and move somewhere more hospitable. You would to if you had a dozen squatters (Munida quadrispina) hanging around your neighborhood all day!
Note: You can see the white ball sponges (Suberites sp.) contracting in the video – the first time this behavior has been captured in situ on the bottom of the ocean. You can check out another time lapse of a contracting sponge done in the lab, Tethya wilhelma, and one of a freshwater sponge Ephydatia muelleri.

Metadata:
Location: Saanich Inlet, 96 m depth
Camera: Olympus C8080WZ
Exposure Settings: 7mm @ F5.6, 1/30s, ISO100, with offcamera strobe in custom housing
Time start: Sept. 14, 2012 @ 07:47:42 UTC
Time end: Oct. 09, 2012 @ 14:47:28 UTC
Total # of images: 1691 8MP still images (3264p x 2448p) taken in doublets (10 s interval) every 30 mins
Workflow:
Images were batched processed to 1440p x 1080p dimensions (Adobe Photoshop) and made into a 15 frames per second (fps) time lapse movie (Avidemux). The time lapse video was then stabilized and re-rendered (Adobe After Effects) because the images did not perfectly overlay on top of one another which resulted in shakey raw footage. Oxygen data profile for the time sequence was downloaded from the VENUS website, processed (Matlab), and plotted (Adobe Illustrator, Adobe Photoshop). The Oxygen profile was then overlaid onto the time lapse video (Adobe After Effects), and an animated time marker was added using keyframes before finalizing the video by pillarboxing into a 1080p HD-video with audio accompaniment (Adobe Premiere Pro).

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Listening to Whale Songs!

by Kara Aschenbrenner

Hydrophone data of orcas, humpback whales and Pacific white-sided dolphin vocalizations can be accessed from www.neptunecanada.com/news/sound-gallery/ or venus.uvic.ca/multimedia-features/hydrophone-highlights/whale-sounds/ .

Orcas. Photo Credit: Francine Mercier, Parks Canada (accessed from: http://www.dfo-mpo.gc.ca/oceans/publications/fedmpa-zpmfed/page01-eng.asp ). The Strait of Georgia is one of the busiest waterways for shipping vessels in Canada and the impacts on killer whales from the underwater noise pollution are of major concern.

Hydrophones (underwater microphones) installed in Folger Passage and the Strait of Georgia, part of the NEPTUNE Canada and VENUS networks, record vocalizations produced by cetaceans. These hydrophone recordings include the songs of transient and resident killer whale pods, humpback whales, fin whales and Pacific white-sided dolphins. The recordings provide scientists with important information about behavior, seasonal migrations, and population shifts (NEPTUNE Canada, 2012).

Pacific white-sided dolphin spotted from the R/V Thompson off of the west coast of Vancouver Island during a cruise for NEPTUNE Canada. Photo credit: NEPTUNE Canada. (Accessed Nov 13, 2012, at neptunecanada.ca/news/news-details.dot?id=35733)

Cetaceans are highly dependent on acoustics as a means of social communication and finding food (echolocation). This is because light can only travel short distances, ~5–20 meters in the water, whereas sound can travel an astonishing 1000 km (VENUS, 2012)! Therefore, the increase in background noise produced by overpassing shipping vessels is a major concern.  Possible impacts to whales from underwater noise exposure include  disturbance and masking of important sounds and hearing damage (Cato et al, 2004).

Spectrogram produced from the VENUS hydrophone array located at the Strait of Georgia East site (170 m depth). Whale sounds are heard during this hydrophone recording. Credit: VENUS Network. (Accessed Nov 13, 2012, at venus.uvic.ca/multimedia-features/hydrophone-highlights/whale-sounds/)

Different cetaceans produce a wide range of unique songs which can be heard with hydrophone recordings. Sounds can be described as whistles, clicks, groans, moans, squeaks and even barks (Seaworld, 2012). For example, dolphins generally sound chatty and produce clicking noises, whereas fin whales have low frequency calls (NEPTUNE Canada, 2012). Songs can also vary between different whale populations depending on which ocean basin they live in (Cato et al, 2000).

References

NEPTUNE Canada (2012). NEPTUNE Canada: An Invitation to Science. Victoria, B.C: University of Victoria.

NEPTUNE Canada, 2012. Website. Accessed Nov.12, 2012: www.neptunecanada.ca/

VENUS, 2012. Website. Accessed Nov. 12, 2012: www.venus.uvic.ca/

Cato, D.H., McCauley, R.D. and Noad, M.J. 2004. Potential effects of noise from human activities on marine animals. Proceedings of Acoustics 2004, Australian Acoustical Society Conference, Gold Coast, 3-5 November. Pp 369-74

Noad, M.J., Cato, D. H., Bryden, M.M. , Jenner, M-N. and Jenner, K.C.S. 2000. Cultural revolution in whale songs. Nature 408 (6812): 537.

Killer Whales. www.seaworld.org/animal-info/info-books/killer-whale/communication.htm. (Accessed Nov 14, 2012).

Oceanographic Data with R: Plot VENUS Network Data

By Allan Roberts

This tutorial provides instructions on downloading raw data from the Victoria Experimental Network Under the Sea (VENUS 2012) and plotting that data with the statistical application R (R Core Team 2012). For this tutorial, I will assume that you have at least some experience with R; however, if you have R installed, and can enter an instruction or two on the command line, that should be enough. If you want to plot data from the NEPTUNE Canada network, refer to my previous post, “How to plot NEPTUNE Canada data with R.” In general, downloading VENUS data is similar to downloading NEPTUNE data, but I did find that there are some differences.

Step 1. Download a data file 

1.1 Go to the VENUS network website:                                     www.venus.uvic.ca

Venus logo

1.2 If you already have an account click on “LOGIN.” (Note: If you have a NEPTUNE Canada account you can use the same e-mail and password to log into the VENUS site.) If you don’t have an account, click on “Register”:

Login

1.3 Click on “DATA” and choose “DOWNLOAD DATA”:

Download VENUS data

1.4 Under “Search Type” choose “Stationary Platform”:

Stationary platform

1.5 Under “Stationary Platform Data” choose “Search by Instrument”:

Search by instrument

1.6 There are gaps in the data record; for this example, I’ve chosen the last two weeks of August, 2012, as an example of a particular interval with available data. Under “Time Range” set the starting and ending date and time, and then click on “Search Active Locations”:

Search active locations

1.7 Under “Location” choose “Saanich Inlet”, “Central Node”, and “VIP-17.” I found these to be the default settings.

Location

1.8 Under “Instrument” choose “Aanderaa Optode 4175 (S/N 1684).” (Again, I found this to be the default setting.)

Anderaa optode

1.9 Under “Sensor(s)” choose “Temperature”:

Select temperature

1.10 Under “Processing” choose “No Averaging”:

No averaging

1.11 Under “Data Format” choose “Comma Separated Value Text File”:

csv file format

1.12 Leave “Metadata” (i.e. documentation) at the default setting of “FGDC HTML”, and click on “Search now”:

Search now

1.13 Wait ….

Requesting data

1.14 Click on the text file….

Data file

… you should get something like this:

Data file output

1.15 Here is one place where I found that downloading VENUS data differed a bit from downloading NEPTUNE data. For the VENUS data, I’ve found that the following works: Copy and paste the downloaded data into a Word file, and then save that file as a plain text file. The plain text file is readable from R. To copy the VENUS data, click on “Select All” …

Select all

… then click on “Copy”:

Copy from Safari

1.16 Paste the file into a Word document. Click on “Save As”; make the document name “VENUS data example”; make the location your desktop, and make the format “Plain Text”:

Save as plain text

When you save as a text file you may get the following warning. (The idea of saving as a text file is that we are not interested in fancy formatting, pictures, etc., we are only interested in the data.) Click “OK”.

File conversion

The result should be a “.txt” file called “VENUS data example” on your desktop:

File icon on desktop

1.17 Create a new folder, called “VENUS network data”, and drop the text file “VENUS data example” into this folder.

VENUS network data

Now that you have the VENUS data saved as a “.txt” file in your “VENUS network data” folder, you are ready to move onto the next step: reading the data file into R.

Step 2. Read the data file into R 

The steps for changing the working directory are the same as in the NEPTUNE data tutorial:

2.1 In the R console type “getwd( )”. This will tell you what your current working directory is:

getwd

2.2 If you are on a Mac click on “Misc”, and choose “Change Working Directory”:

set working directory mac

If you are on a PC, click on “File”, and choose “Change dir …”:

set working directory pc

2.3 If you are on a Mac, browse for the “VENUS network data” folder, click on it, and click on “Open”; if you are on a PC browse for the “NEPTUNE data” folder, click on it, and click on “OK.”

2.4 In the R console, type “getwd( )”; the “VENUS network data” folder should now be your working directory:

wd again with correct wd

2.5 Open the text file, and look at it. We want to skip all the documentation lines before the first line of data. For this example, there should be 15 lines. This includes the line with the variable names. (The variable names are not yet formatted for R; variable names in R need to be without spaces.)

read file skip 15 lines header false

2.6 Check the downloaded data by entering “head(data)”; this will show the first few lines of the data frame. (To see all the data, just type ”data”, and press enter.)

show data

2.7 To give names to the columns, type:

give names to columns

Enter “head(data)” again, and you should see names at the tops of the columns. (For this tutorial, we are not concerning ourselves with the flag variable in the third column.)

data with labels

Now that the data have been downloaded, you are ready to move onto plotting …

 

Step 3. Plot the data 

3.1 For a rough plot of the data, type:

rough plot code

rough plot

3.2 To plot the data as a line graph with a title, and with better axis labels, we can use two steps. First: The following command will plot the data without axis labels, and make the graph a line graph in blue.

line graph code

Second: Leave the graphics window open, and enter a command to add the title and axis labels.

Add title line

You should get a graph like the one below. I’ve found that the easiest way to put a graph made in R into a written document or slide show is to click on the graphics window and then use copy and paste.

final graph

3.3 Now go explore the other data available from the VENUS network!

Citations

VENUS, 2012. Website. Last accessed Oct. 17, 2012: www.venus.uvic.ca

R Core Team (2012). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.