Preparing the cod-ends of our coupled 4+1 m² MOCNESS onboard R/V Sikuliaq in 2018 (© Mark Farley)
Research Associate
Oregon State University, Hatfield Marine Science Center
Moritz S. Schmid, PhD
Underwater imaging, deep learning, and plankton ecology at Oregon State University
Welcome!
I am a Research Associate at the Hatfield Marine Science Center, Oregon State University, working on plankton ecology. In the lab of Prof. Su Sponaugle and Prof. Bob Cowen we investigate plankton using underwater imaging, in conjunction with deep learning in order to analyze the hundreds of millions to billions of plankton images we gather on a cruise. Using the resulting fine-scale data on the distribution of plankton ranging from diatoms over various copepods to larval fish and siphonophores, we ask novel ecological questions. Current projects include work on 1) the effects of intermittent and continuous upwelling on trophodynamics (with a focus on larval fish) off the Oregon and California coasts, 2) investigating how fine-scale vertically stratified plankton data can inform seascapes, as well as 3) streamlining and unifying the efforts of different underwater imaging laboratories (and their processing pipelines) from around the world. More research and all lab members are described here: http://hmsc.oregonstate.edu/research-labs/planktonlab.
For my PhD in Arctic oceanography I worked with my supervisors Prof. Louis Fortier and Prof. Marcel Babin at the Takuvik Joint International Laboratory (CERC in Remote Sensing of Canada’s New Arctic Frontier), Université Laval, Québec, Canada.
There, I worked on the spatiotemporal variability of mesozooplankton and coupling with their phytoplankton food in the Canadian Arctic. To reach my study goals I utilized a new optical underwater imaging system (Lightframe Onsight Keyspecies Investigation, LOKI) and machine learning algorithms. I developed an automatic species recognition model, down to the developmental stage of species, which can reliably turn images into taxonomic information. I then used that model to further work on the links between individual copepod lipids and the copepods’ diapause. As part of my PhD I also described intriguing fine vertical scale (1 m resolution) Calanus species interactions. Calanus hyperboreus showed substantially different distribution peaks, in the subsurface chlorophyll maximum, from C. glacialis. The findings of my PhD are described in three research papers listed in the publications section.
For my M.Sc. thesis in International Nature Conservation I worked on spatial predictive modeling of pan-Arctic zooplankton. I used present time and future environmental data to predict zooplankton parameters like depth distribution and presence/absence into the future (max. year 2100). Future data was taken from the Canadian Earth System Model 2 (CanESM2), 5th generation IPCC data. I did this work at the University of Alaska Fairbanks
Other research interests are described briefly on the research page or are documented in my CV.
Professional Experience
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ongoing2020
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20202017
Postdoctoral Scholar
Oregon State University, Hatfield Marine Science Center
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20162013
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20092009
Research assistant
Max-Planck-Institute (MPI) for Biophysical Chemistry, Göttingen, Germany
Education
- Ph.D. 2017
Ph.D. in Oceanography
Université Laval, Canada
- M.Sc. and M.I.N.C. 2012
Master of International Nature Conservation (M.I.N.C.)
University of Alaska Fairbanks, USA; University of Lincoln, New Zealand; University of Göttingen, Germany
- B.Sc. 2010
Bachelor of Biology
University of Göttingen, Germany
Other certifications
Coursera, taught by Roger Peng et al., Johns Hopkins University
Coursera, taught by Andrew NG, Stanford University
Introduction to interactive programming in Python (part 1), Coursera, taught by Joe Warren et al., Rice University
Introduction to interactive programming in Python (part 2), Coursera, taught by Joe Warren et al., Rice University
Select Awards, Scholarships & Grants
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Jan 2017Invitation to Arctic Frontiers Emerging LeadersThe Arctic Frontiers Emerging Leaders program 2017 was centered around the debate of how the Arctic, its people, and industry can transition to a blue future/economy. The emerging leaders program included workshops, presentations, and debates, and was very multidisciplinary. Some of the areas represented were commercial fisheries, high level politics, European aerospace, military, academia, petroleum(industry), social sciences, as well as indigenous peoples. The invitation to the Emerging Leaders program included a large scholarship.
https://cirfa.uit.no/emerging-leaders-of-arctic-frontiers-2017/
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Nov 2016John W. Davies Memorial Award from the SNAMES (Arctic Section)Received this award from the Society of Naval Architects and Marine Engineers, Arctic Section (SNAME AS) for studies on underwater imaging of plankton in the Arctic and the development of a machine learning model which automatically identifies species on images.
http://www.sname.org/arcticsection/scholarshipinfo/pastrecipients -
JUN 2016Award for excellence in doctoral studies (Fonds Richard-Bernard)Received the Bourse Richard-Bernard by Université Laval, marking excellence in doctoral studies in the biology department. http://www2.ulaval.ca/fondation/faire-un-don/fonds.html?fonds=142
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NOV 2014Best oral presentation awardReceived the Best Oral Presentation Award at the Québec-Océan conference 2014 for my presentation: “Automated zooplankton identification for the North Water Polynya and adjacent waters”.
Read the announcement in Québec-Océan’s newletter :
http://www.quebec-ocean.ulaval.ca/pdf_xls_files/Bulletin14.pdf -
JAN 2013Outstanding Poster Presentation Award
Outstanding Poster Presentation Award at the 2013 Arctic Frontiers Conference, Tromso, Norway. Title: “Assessing spatiotemporal variability in the mesozooplankton using a newly developed plankton imaging system”. Read the announcement here: http://www.quebec-ocean.ulaval.ca/pdf_xls_files/Newsletter9.pdf -
SEP 2012Award to participate in the AWI summer school: Climate Change in the Marine Realm
This international climate school was organized by the Alfred-Wegener Institute (AWI) in Germany and touched various aspects of climate change in the marine realm such as the physical basis, mitigation efforts, case studies on coastal erosion and more. Award approx. 1.500€. -
2012 - 2015Takuvik Doctoral ScholarshipTakuvik scholarship from the CERC in Remote Sensing of Canada’s New Arctic Frontier, 10,000$/year.
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2012 - 2014Scholarship for Excellence in Leadership and Sustainable Development - Scientific Leadership
Universite Laval awarded me this scholarship of 10,000$ per year for excellence in scientific leadership. The scholarship was sponsored by the ``Syndicat des professeurs et professeures de l’Université Laval``. The initial funding period of 2012-2013 was renewed for the period of 2013-2014. -
APR 2012 - OCT 2011Otto Bayer Fellowship to study at the University of Alaska Fairbanks
Reception of a Otto Bayer Fellowship from the Bayer Foundation for studies at the University of Alaska Fairbanks on future predictions of zooplankton, 7.000 € -
FEB 2011ISAP fellowship from the German Academic Exchange Service to study in New Zealand
ISAP (``Internationale Studien- und Ausbildungspartnerschaften``) fellowship from the German Academic Exchange Service to study in New Zealand for my M.Sc. ISAP translates to International Study and Training Partnerships, 5.500€.