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Software 2017-04-29T04:14:43+00:00

Tethys

Tethys is a scientific workbench that allows the integration of acoustic detections, classifications, and localizations of aquatic animals with environmental data from a wide variety of souces. We and our collaborators built Tethys as we saw the opportunity to build systems that will let us analyze long-term data sets. Frequently, people analyze a few seasons worth of data and publish the results. While the summary results are archived in the publication, detailed results that could be used in subsequent analyses are lost. Tethys lets researchers preserve detailed information and provides simple acces to environmental data. Learn more at the Tethys web site.

Silbido

Silbido is an automated whistle extraction system for toothed whales and dolphins.

The methods used are described in:

M. A. Roch., T.S. Brandes, B. Patel, Y. Barkley, S. Baumann-Pickering, M.S. Soldevilla (2011) Automated extraction of odontocete whistle contours. J. Acous. Soc. Am., 130(4), 2212-2223.

Requirements: Matlab 2008b or later, Signal and Image processing toolboxes.

System testing and development were performed on 64 bit linux and Windows systems, with some testing done on 32 bit systems. A few functions use the Mex interface which permits Matlab to interface to code written in C/C++. As this depends on the type of machine and operating system that you are using, you might need to compile these using Matlab’s mex function and one of the freely available supported compilers (After running mex -setup, just type mex and the C/C++ file name at the Matlab prompt.). For Microsoft Windows users, you might also need Microsoft’s Visual Studio Runtime Development for 2008 and 2010 (freely available from Microsoft), libraries that are used by code compiled with these libraries.

We provide the following versions of silbido (we recommend beta 2):

  1. The baseline version that is very close to the one used in Roch et al. 2011 and will produce nearly the same results.
  2. The beta versions that have updated interfaces. Beta 1 (2014-07-15) provides similar results to the baseline, beta 2 (2015-03-11) represents work to reduce the false positive rate as well as additional user interface changes..

In addition, an extended version of the file format has been released (4/16/2013) that was used in the 2013 DCLDE conference in St. Andrews. Download file read/write Matlab/Java software only.

Regardless of which system you use, you will need to take some preliminary steps to set things up and you should these instructions which are from the beta version. With the exception of references to other instruction manuals, these instructions apply to either system.

Both systems are also bundled with a version of triton, Matlab software developed by Sean Wiggins at the Scripps Whale Acoustics Lab (SWAL) that has been heavily modified by us and includes our echolcoation click detectors. You do not need to use triton unless you want to (we like it), but we use some of the functionality from triton in silbido although we have not yet integrated it into Triton. The most recent version of triton is available from SWAL.

You can obtain data for silbido from MobySound. John Hildebrand (Scripps Institution of Oceanography) and I have made the data and annotations that were used for the above article (along with many more) available as part of the dataset for the 5th International Workshop on the Detection, Classification, and Localization of Marine Mammals Using Passive Acoustic Monitoring. The data may and annotations may be found in the Workshop data section of Dave Mellinger’s MobySound┬ásite.