[MARMAM] New publication: Advanced image recognition: a fully automated, high-accuracy photo-identification matching system for humpback whales

[Ted Cheeseman]

Dear MARMAM readers, on-behalf of my co-authors, I am pleased to share our new 
publication:


Advanced image recognition: a fully automated, high-accuracy 
photo-identification matching system for humpback whales. 



Authors: Cheeseman T, Southerland K, Park J, Olio M, Flynn K, Calambokidis J, 
Jones L, Garrigue C, Frisch Jordán A, Howard A, Reade W, Neilson J, Gabriele C, 
Clapham P (2021) 

Mamm Biol 2021 1–15. doi: 10.1007/S42991-021-00180-9

An online (but not downloadable) full version is available here: 
https://rdcu.be/cCOtw or send me an email if you’d like a pdf

We describe the development and application of a new convolutional neural 
network-based photo-identification algorithm for individual humpback whales 
(Megaptera novaeangliae). The method uses a Densely Connected Convolutional 
Network (DenseNet) to extract special keypoints of an image of the ventral 
surface of the fluke and then a separate DenseNet trained to look for features 
within these keypoints. The extracted features are then compared against those 
of the reference set of previously known humpback whales for similarity. This 
offers the potential to successfully automate recognition of individuals in 
large photographic datasets such as in ocean basin-wide marine mammal studies. 
The algorithm requires minimal image pre-processing and is capable of accurate, 
rapid matching of fair to high-quality humpback fluke photographs. In real 
world testing compared to manual image matching, the algorithm reduces image 
management time by at least 98% and reduces error rates of missing potential 
matches from approximately 6–9% to 1–3%. The success of this new system permits 
automated comparisons to be made for the first time across photo-identification 
datasets with tens to hundreds of thousands of individually identified 
encounters, with profound implications for long-term and large population 
studies of the species.

…or more succinctly: we built a magic box that can ID most any humpback whale 
fluke nearly instantly and have now aggregated in Happywhale.com a database of 
over 64000 individuals in one global dataset. We believe this tool is bettering 
the lot of marine conservation; that’s the goal.

Yay whales :)
Ted

—
Ted Cheeseman
t...@happywhale.com
www.Happywhale.com
https://www.facebook.com/happywhales/

** know your whales :) **

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[MARMAM] New publication: Subsurface swimming and stationary diving are metabolically cheap in adult Pacific walruses (Odobenus rosmarus divergens)

[Alicia Borque Espinosa]

Dear marmamers,
My coauthors and I are pleased to announce our recent publication in the 
Journal of Experimental Biology. The objective in the present study was to 
provide novel data about metabolic demands on the Pacific walrus, which could 
help understand the potential impacts of environmental change. In this study we 
report measured metabolic rates in adult female Pacific walruses while floating 
in water and during stationary dives and subsurface swimming. The data show 
that the underwater activities did not increase metabolic costs above those 
while floating in water.
Citation:
Alicia Borque-Espinosa, Karyn D. Rode, Diana Ferrero-Fernández, Anabel Forte, 
Romana Capaccioni-Azzati, Andreas Fahlman; Subsurface swimming and stationary 
diving are metabolically cheap in adult Pacific walruses (Odobenus rosmarus 
divergens). J Exp Biol 1 December 2021; 224 (23): jeb242993. doi: 
https://doi.org/10.1242/jeb.242993
Abstract:
Walruses rely on sea-ice to efficiently forage and rest between diving bouts 
while maintaining proximity to prime foraging habitat. Recent declines in 
summer sea ice have resulted in walruses hauling out on land where they have to 
travel farther to access productive benthic habitat while potentially 
increasing energetic costs. Despite the need to better understand the impact of 
sea ice loss on energy expenditure, knowledge about metabolic demands of 
specific behaviours in walruses is scarce. In the present study, 3 adult female 
Pacific walruses (Odobenus rosmarus divergens) housed in professional care 
participated in flow-through respirometry trials to measure metabolic rates 
while floating inactive at the water surface during a minimum of 5 min, during 
a 180 s stationary dive, and while swimming ∼90 m horizontally underwater. 
Metabolic rates during stationary dives (3.82±0.56 l O2 min−1) were lower than 
those measured at the water surface (4.64±1.04 l O2 min−1), which did not 
differ from rates measured during subsurface swimming (4.91±0.77 l O2 min−1). 
Thus, neither stationary diving nor subsurface swimming resulted in metabolic 
rates above those exhibited by walruses at the water surface. These results 
suggest that walruses minimize their energetic investment during underwater 
behaviours as reported for other marine mammals. Although environmental factors 
experienced by free-ranging walruses (e.g. winds or currents) likely affect 
metabolic rates, our results provide important information for understanding 
how behavioural changes affect energetic costs and can be used to improve 
bioenergetics models aimed at predicting the metabolic consequences of climate 
change on walruses.
The journal provided open limited downloads by using the following link:
https://journals.biologists.com/jeb/article/doi/10.1242/jeb.242993/273684/Subsurface-swimming-and-stationary-diving-are?guestAccessKey=a9080811-7e8a-4a63-b785-63a83d25b59f
Please, feel free to contact (ali_...@hotmail.com) 
for any comment, question or for a PDF copy of the manuscript.
Kind regards,
Alicia Borque Espinosa
PhD Candidate, Universitat de València & Fundación Oceanogràfic de la Comunitat 
Valenciana.
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[MARMAM] Online Course - An Introduction to Basic Statistics for Biologists using R - 17th to 20th January 2022

[cdmacleod]

Data preparation and analysis is a key skill for all those working with 
marine mammals, and of the available software packages, R has rapidly 
become the most widely used. This means that a knowledge of how to 
prepare and analyse data in R is essential skill for marine 
mammalogists.


We will be running an instructor-led online course in January 2022 based 
around our latest book, _An Introduction to Basic Statistics for 
Biologists using R_. It will be held over Zoom video-conferencing and 
will provide all the practical knowledge and experience you need to get 
started with analysing biological data using R. As a result, no previous 
experience with R or statistical analysis is required to do this course.


It will run from the 17th to the 20th of January 2022. The course will 
consist of four three-hour sessions, and one session will need to be 
completed each day. However, you will have a choice of completing it 
between 10:00 and 13:00 UK Time (primarily for those living in Europe, 
Asia and Africa) or 18:00 to 21:00 UK Time (primarily for those living 
in North and South America). This choice of time slots for each session 
allows participants from as wide a range of time zones to participate in 
the course.


Attendance will be limited to a maximum of 24 people per session. The 
fees for this course are GBP 250 per person (with a discounted rate of 
GBP 195 for students, the unwaged and those working for registered 
charities). To book a place, or for more information, you can either 
email us at i...@gisinecology.com or click on the link below.


http://gisinecology.com/stats-for-biologists-1/live-online-course-an-introduction-to-basic-statistics-for-biologists-using-r/

About the Course:

This is a practical course and it is aimed at anyone who wishes to learn 
how to carry out basic data processing and statistical analyses on 
biological data using R. This includes importing data sets into R, 
error-checking and processing them to prepare them for analysis, 
calculating basic summary statistics, creating graphs, assessing and 
transforming their distributions, and running statistical tests such as 
Shapiro-Wilk tests, t-tests, Mann-Whitney U tests, paired t-tests, 
Wilcoxon Matched Pairs tests, F-tests for equality of variance, Levene's 
tests, ANOVAs, Kruskal-Walis tests, chi-squared tests, correlations and 
linear regressions. It will also cover how to use R, how to work out how 
to do things for yourself in R and how to create annotated R script 
archives of what you have done.


Each session will consist of a series of background talk covering 
specific topics (more details are provided below), followed by related 
practical exercises based on instructions from An Introduction to Basic 
Statistics for Biologists using R. As a result, all participants will 
receive a free copy of this book shipped to their address in advance of 
the start of the course. While you are encouraged to remain online 
during the practical sessions, you can choose to go off-line as you work 
though the exercises (or if you need to take a break). However, if you 
have any questions, the course instructor will be available throughout 
the course for you to ask any questions you wish at any point.


This course will be hosted by Dr Ross MacLeod, one of the authors of _An 
Introduction to Basic Statistics for Biologists using R_.


At the end of the course, all attendees will receive a certificate of 
attendance and completion. Each certificate is embossed with the GIS In 
Ecology official stamp to prevent its fraudulent reproduction. In 
addition, each certificate has its own unique identification number that 
we will record, along with your name, meaning that we can verify the 
authenticity of the certificates we issue (and the course you have 
completed) on request.


---

==
GIS IN ECOLOGY - Providing Training, Advice And Consultancy On The Use 
Of GIS In Ecology


Web: www.GISinEcology.com [1] Email: i...@gisinecology.com

Need to ask a question about using GIS? Try the GIS In Ecology Forum: 
www.GISinEcology.com/GIS_in_Ecology_forum.htm [2]


Books From GIS In Ecology Staff:

GIS For Biologists: A Practical Introduction For Undergraduates; RRP: 
£24.99
An Introduction To Integrating QGIS And R For Spatial Analysis; RRP: 
£19.99
An Introduction To Species Distribution Modelling (SDM) Using QGIS And 
R; RRP: £19:99


If you wish to purchase these books, visit: 
http://www.gisinecology.com/book-shop/


To help the environment, please do not print out this email unless it is 
unavoidable.

==

Links:
--
[1] http://www.GISinEcology.com
[2] http://www.GISinEcology.com/GIS_in_Ecology_forum.htm___
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[MARMAM] Job Announcement: Research Scientist Effects of Seismic Surveys on Harbour Porpoise (GEOSTOR)

[Dähne Michael Dr .]

Dear Colleagues,

I would like to share the following position with you:

Research Scientist (m/f/d): Potential Effects of Carbon Capture Storage and 
Seismic Surveys on Porpoises (GEOSTOR)

The foundation Deutsches Meeresmuseum is a national and internationally 
important, specialized natural history museum and is one of the most visited 
museums in Germany. Its exhibition, collection and research activities focus on 
marine biology, fisheries and marine aquariums. The foundation Deutsches 
Meeresmuseum includes the exhibition sites MEERESMUSEUM and OZEANEUM in 
Stralsund as well as the NATUREUM and the NAUTINEUM.
The growing research department of the Deutsches Meeresmuseum focuses on 
aquatic vertebrates, European seas and collection-related research. The German 
Oceanographic Museum has a long-standing expertise in acoustic monitoring and 
the effects of underwater sound on marine vertebrates.

The GEOSTOR project aims to develop a roadmap for large-scale storage of carbon 
in sub-seabed geological formations in the German sector of the North Sea. It 
will quantify geological storage potentials, identify and investigate possible 
storage locations, assess environmental risks, develop novel monitoring 
techniques, study the legal framework and estimate costs for offshore CO2 
transport and storage. Part of the environmental risks are effects on the 
distribution, abundance and physiology of harbor porpoises by an increased need 
for seismic exploration as part of the monitoring of potential deposits. The 
project is funded by the Federal Ministry for Science and Education.

Your tasks:
• Evaluation of a large dataset of broad band recordings and click detector 
data of odontocete echolocation during seismic surveys
• Modelling of porpoise distribution in relation to a seismic source
• Development of sound exposure maps
• Establishing guidance documents and mitigation strategies to protect 
porpoises during seismic surveys
• Support in project management and administrative processing including 
budgeting, monitoring of project finances and project control
• Quality assurance, documentation of results and reporting
• Organization of project meetings and scientific conferences
• Representation of the museum at external events with a focus on research
• Cooperation and collaboration in various national and international committees
• Publication of research results in internationally peer-reviewed journals
• Presentation at symposia
• Work at sea to collect data

Your profile:
• PhD in bioacoustics, physics, engineering or biology
• Strong background in underwater acoustics, and/or ecological modelling
• Proven programming skills in Matlab or R
• Excellent English written and oral communication skills and either German 
Language skills of the willingness to learn German
• Experience in sound propagation modelling
• (optional) Biostatistics including Generalized Additive Mixed Models (GAMM) 
and Generalized Estimating Equations (GEE), or equivalent
• (optional) experience in evaluating data from acoustic monitoring
• (optional) experience in working towards a political framework for regulation

We offer:
an ambitious, variable job in a young team of biologists, veterinarians, 
educators and engineers working in a complex field of conservation challenges, 
public relation work, collections based research, exhibitions and outreach 
activities. The Museum is furthermore an equal opportunity employer.

The salary is in accordance with TVöD VKA and is remunerated at EG 13 with a 
regular weekly working time of 39,5 (in 2022) and 39 (from 2023) hours per week 
(full-time).
Please send your complete application as a single PDF file with letter of 
motivation as well as statement of research experience, including publications 
and third-party funding by e-mail together with your references and 
certificates by December, 31, 2021 to:

Deutsches Meeresmuseum E-Mail: bewerb...@meeresmuseum.de
Dr. Michael Dähne
Katharinenberg 14–20
18439 Stralsund

For any questions please contact Dr. Michael Dähne, Tel. +49 152 3890 3160, 
michael.dae...@meeresmuseum.de.
Costs incurred in connection with this job advertisement will not be reimbursed.

I hope this position will find your interest!

Kind regards,
Michael Dähne

--
Dr. Michael Dähne
Kurator für Meeressäugetiere/ Curator of Marine Mammals

Deutsches Meeresmuseum
Museum für Meereskunde und Fischerei ∙ Aquarium
Stiftung des bürgerlichen Rechts Katharinenberg 14 – 20
18439 Stralsund

Tel.:  +49 (0) 3831 26 50 310
Fax:  +49 (0) 3831 26 50 309
Mail:  michael.dae...@meeresmuseum.de
Web: www.deutsches-meeresmuseum.de
Direktorium
Prof. Dr. Burkard Baschek
Andreas Tanschus

Ust. ID Nr.: DE 162 772 269
Steuernr.: 082/126/00068
Hinweis zum Datenschutz:
www.deutsches-meeresmuseum.de/datenschutz

Postanschrift/Postal adress:
Katharinenberg 14 -