CATS prh step-by-step video tutorial (first presented at BLS7)
Biologging tags are capable of capturing high-resolution data from cryptic species that spend a significant portion of their lives in remote or inaccessible environments, such as below the sea surface. The advancement of biologging technologies over the last ~30 years has lead to an explosion of research into the hidden lives of these elusive animals. Information about locomotion, feeding, migratory patterns, reproduction, and metabolism have all been determined using data obtained with biologging tags. CATS (customized animal tracking solutions) tags are one of the newest platforms for this type of research and integrate high-resolution video with a suite of inertial and environment sensors.
For the last 5 years, we as members of the Goldbogen lab at Stanford University's Hopkins Marine Station have been using CATS tags to study the biomechanics and behavior of large baleen whale species. In the course of this work, we have tested and streamlined a workflow and set of tools to integrate multiple streams of raw sensor data into a simple data packet that can be used for further analyses.
The tool kit works primarily with Matlab and includes tools to read/write, calibrate, process, visualize, and carry out statistical analysis of datasets. These tools are based on many of the tools designed at animaltags.org, but extend these ideas into a single tag processing workflow. The tools can work with a variety of tags (e.g. Acousonde, openTags, TDR-10) and are focused on CATS tags as models for video/data integration. The basic processing framework is also suitable for a variety of species, though our lab focuses primarily on large cetaceans.
Software and Data
The tag tool kit requires Matlab software and users will be required to have a computer with Matlab installed and ready to use. Matlab 2014a, 2020, or Student versions will be compatible with the tool kit.
Other software that is suggested to download and have basic familiarity with (all free) includes: VLC media player, ffmpeg, Audacity, Google Earth, BORIS, Trackplot, as well as any appropriate UIs from CATS. We also use Microsoft Excel for some applications, but other spreadsheet software can also work (e.g. Open Office). Support for Mac operating systems is limited, but software should theoretically be implementable on macs as well.
The toolkit (including all scripts and template files) and a "wiki" style tutorial is available through Github: https://github.com/wgough/CATS-Methods-Materials
Practice data will be available from Data Dryad at the following link: https://datadryad.org/stash/share/KFi8G5QC7DFPYXynQeSotxtXqANZL70LFUGEiiDTSMU
See the "Code and Materials" section of this website for more information and additional links.
Please direct all questions to Will Gough (firstname.lastname@example.org) or Dave Cade (email@example.com). We will also have weekly CATS Tag Office Hours on Thursdays (times TBD). Please join us at the following zoom link to ask any questions that you may have about the CATS toolkit or biologgin tag analysis in general.