Torsten Linders – ODF Sweden

Ocean Data Survey Sweden 2023

Torsten Linders — Fri, 08 Dec 2023 10:35:14 +0000

We are excited to open the Ocean Data Survey Sweden 2023, an annual survey conducted by ODF Sweden on the ocean data landscape in Sweden in close collaboration with over 100 industry, public sector, and academic organizations. This survey aims to illuminate the challenges, trends and technologies of ocean data users in order to identify, discuss and evaluate potential solutions to benefit the ocean data community at large. 2023 will be the first iteration!

The survey is open now and closes on ~~31 December~~ 15 January 2024, 23:59 Swedish time. You reach it by this link or by the QR code at the top, or directly in the frame below. Feel free to share with colleagues in your network. The survey targets organisations and individuals based in Sweden or working with Swedish data.

All questions are completely anonymous, there are 32 multiple choice, plus one open ended question. The survey is managed by four ODF Sweden partners: Swedish National Data Service and data science consultancy Combine AB, together with Chalmers University of Technology and University of Gothenburg. The result will be published in January 2024, here on the ODF Sweden website.

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Subsea image analysis: A first national consortium assembled!

Torsten Linders — Mon, 06 Mar 2023 12:49:25 +0000

(post written by Matthias Obst, first published at Zooniverse)

In early March 2023 we assembled for the first time a national consortium around subsea image analysis for marine biology research and monitoring. The meeting brought together major national data providers such as the Swedish Meteorological and Hydrological Institute (SMHI), the Geological Survey of Sweden (SGU), Swedish National Dataservice (SND), the Swedish Agency for Marine and Water Management (SwAM), and the Swedish Biodiversity Data Infrastructure (SBDI). We also had several partner companies and NGO’s participating who actively work in the field of marine environmental monitoring (Combine, BeGeospatial, SeAnalytics, Medins, Wildlife.ai) as well as academic institutes (Lund University, University of Gothenburg).

The objective of the meeting was to explain the current state of the KSO image analysis system, present scientific use cases, and discuss plans for further development and integration with existing research infrastructures.

The workshop was a great success! We presented and discussed tangible use cases including applications for habitat mapping, community composition analysis, invasive species impact assessments, fish stocks estimations in marine protected areas, and environmental impact assessments in relation to wind park construction. Based on the agreements we achieved in the workshop we will now work towards user support as well as consolidation and documentation of the infrastructure services for use in ecological research and biological monitoring in Sweden.

More about subsea image analysis

For all of you who like to use the system or want to know more about it, just contact us or find more information and updates here:

• Information page
• Main repo
• Jupyter notebooks (try them by pressing the “Open in Colab” button)
• Current citizen science challenge

The development of the system is currently financed by the FORMAS project PLAN SUBSIM, the VINNOVA project Ocean Data Factory, as well as the VR infrastructure program Swedish Biodiversity Data Infrastructure (SBDI), and the European Digital Twin of the Ocean program (DTO).

Use cases in PLAN-SUBSIM

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ODF Sweden innovation cycle #7: The do-it-ourselves challenge!

Torsten Linders — Tue, 07 Feb 2023 19:55:38 +0000

We are now moving forward with our next innovation challenge! Cycle #7 will be the ‘To-do-it-ourselves challenge‘. We start with this challenge now and the cycle is expected to last at least until the summer this year. The core activities of challenge #7 will be to build and deploy ocean sensors and a leading partner will be Chalmers Revere Lab. An important purpose in this cycle is also to proceed further with our previous cycles on data availability and citizen science.

From these previous cycles, we take some specific knowledge with us. In cycle #5 (‘the data availability challenge‘), we learnt the need to take a long perspective on data availability and FAIRness (Findable, Accessible, Interoperable, Reusable). In cycle #6 (‘the citizen science challenge‘) we learnt about reaching out and making partners with new groups and individuals, to leverage our own and other’s competence and resources.

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Grand Meeting on 17 October!

Torsten Linders — Thu, 22 Sep 2022 09:34:53 +0000

New starting place, see this map:

ODF Sweden exists in real life, not only online! This fall we decided to have our Grand Meeting on site. A real life meeting not only means that we can have real coffee and sweet bread (‘fika’ is important in Sweden…). We will also get the chance to see with our own eyes and put our hands on some fascinating items. We will be hosted by the Chalmers Revere Lab, at Lindholmen in Gothenburg. Send us a line if you have not got an invitation and you want to join us 17 October, 1 – 5 pm, Valdemar Noréns gata 12.

Revere will demonstrate some of their work on maritime automation and ocean data acquisition and analysis. We are excited to be hosted by this dynamic group, combining expertise in cyber-physical systems and AI, with curiosity and a can-do mentality (“we have worked a lot with self-driving cars, but that started to feel a bit done…”)

Below is a promo video for the experimental Seacat surface drone, which Revere has been instrumental for building, together with several other ODF Sweden partners.

We are also happy to welcome a group from Oceanlab at OsloMet in Norway. Oceanlab is made up of researchers from around the world with backgrounds in marine robotics, machine learning, electrical engineering, and operations research.

In this Grand Meeting we build on the considerable experience we have gained from our five previous innovation cycles (notably the fifth, The Data Availability Challenge), we focus on what have at hand in the ongoing sixth cycle (The Citizen Science Challenge), and we look at ideas of where we want to go from here…

Updated programme:
13:00 to 13:10 – Welcome outside at quay (at the waterside of the TV house, map)
13:10 to 14:00 – Revere Lab. Demo on water and presentation inside lab. Platforms with massive sensor suits.
14:00 to 14:10 – Break
14:10 to 15:00 – OsloMet/Oceanlab presentation and display. Diving robots and underwater observatories with many cameras.
15:00 to 15:10 – Break
15:10 to 16:00 – ODF status updates and Seventh Cycle. (and perhaps something about sailing and bottom crawling robots…)
16:00 to 17:00 – Optional ODF Workshop and discussion (Camera projects & Seventh Cycle)

Logistics:
The meeting will be on site at Lindholmen, in Gothenburg.
We are not planning for remote participation this time.
We will be hosted by Chalmers Revere Lab (map)
The meeting will start 1 pm at the waterside (map) outside the TV house, 450 meters from Revere Lab.

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PLAN-SUBSIM studies interactions between invasive and native fish

Torsten Linders — Thu, 25 Aug 2022 10:38:49 +0000

Photo above by Leon Green. Round gobies and many other species of fish observed using baited remote underwater video (BRUV).

This spring scientists at the University of Gothenburg started to investigate the interaction between invasive and native fish on the Swedish west coast. The activity is part of the ODF Sweden project PLAN-SUBSIM. A large part of the data collection takes place through underwater video recording and Koster Seafloor Observatory (KSO) will be used to streamline the analysis of the many hours of video recordings. “Invasions from alien species are expected to increase in the future, so it is absolutely critical that we learn how to use such new image analysis services” says Leon Green who studies how biodiversity can limit the spread of alien species.

This is an important step for KSO and PLAN-SUBSIM: Developing algorithms for automatically identifying moving species such as fish with fixed observatories. Challenging, but fun, it requires partly new ways of collecting and analysing video data

Mathias Obst Docent, SeAnalytics AB, and University of Gothenburg

...especially the combination big data methods and citizen science can become an important toolkit for mapping the distribution and population growth of invasive fish.

Leon Green Researcher, University of Gothenburg

About PLAN-SUBSIM, KSO and invasive fish

PLAN-SUBSIM homepage.
Koster Seafloor Observatory (KSO) at the Zooniverse citizen science platform.
Predators and biodiversity as biocontrol of the invasive round goby (news post at University of Gothenburg).
Leon Green: I have a particular interest in invasive species (news post at University of Gothenburg).
Student and research projects based on KSO.
Performance example of first object detection models for benthic fauna and habitat builders, from PLAN-SUBSIM

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PLAN-SUBSIM delivers first object detection models for benthic fauna and habitat builders

Torsten Linders — Mon, 13 Jun 2022 08:19:57 +0000

ODF Sweden project PLAN-SUBSIM is ticking along nicely! First and second user workshops have been held, and now comes a report describing a first object detection models for benthic fauna and habitat builders.

Report summary

The increasing access to autonomously operated technologies offer vast opportunities to sample large volumes of biological data. However, these technologies also impose novel demands on ecologists to apply efficient tools for data management and processing, which are publicly available and easy to use. In order to address these needs Ocean Data Factory Sweden (ODF) and Swedish Biodiversity Data Infrastructure (SBDI) develop a national platform for analysis of subsea images (PLAN-SUBSIM). The system is named Koster Seafloor Observatory (KSO) and combines several essential functions for analysing large volumes of subsea image data for marine ecological research in Sweden. The system has now finished its 3^rd developmental cycle which produced open-source services to upload, explore, and manage image subsea classifications, as well as train and test object detection models.

The third cycle also included a number of scientific collaborations with Geological Survey of Sweden (SGU) and Medins AB on sea bed monitoring in the Kattegat and Baltic sea. As a result, we can now offer a first suite of object detection models for 5 key ecological species, including sea pens (Pennatula phosphorea, Virgularia mirabilis), the Deeplet sea anemone (Bolocera tuediae), the cold-water coral (Desmophllum pertusa), and blue mussels (Mytilus spp.). The models are verified, well documented, and ready for use in ecological research and seafloor monitoring in Swedish coastal waters. An example of model performance can be found here, while our model zoo is accessible here.

Image credits: Koster Seafloor Observatory.

About PLAN-SUBSIM

Project homepage.
Bachelor thesis on the effect of trawling on sea pens in Kattegatt (pdf, in Swedish).
Performance example of first object detection models for benthic fauna and habitat builders.

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ODF Sweden 2.0

Torsten Linders — Fri, 08 Oct 2021 19:19:44 +0000

Today the Swedish Innovation Agency (Vinnova) decided to fund ODF Sweden for another two years, 2022 – 2023. We are of course delighted and proud about the confidence Vinnova is showing us. We will continue to function as Sweden’s national ocean data lab, fostering innovation in the sustainable Blue Economy, and increasing the usage of ocean data.

Now ODF Sweden will step up our game. We are a fantastic group of partners, boundary spanning data scientists, maritime entrepreneurs, and ocean observers. Together we do magic!

Robin Teigland

Professor, Director of ODF Sweden

ODF Sweden Partners:

(Do you want your organisation on this list? Please contact us!)

In addition, ODF Sweden has formed partnerships with the Swedish Agency for Marine and Water Management (SwAM) and Swedish Maritime Administration (SMA), and is working with other organizations, such as AI Sweden.

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ODF: Where AI meets the ocean

Torsten Linders — Wed, 15 Sep 2021 14:59:24 +0000

What has made ODF Sweden such a success? One answer is definitely that in ODF data scientists collaborate closely with ocean data experts. Most often that collaboration takes place around tables and computers and white boards: Discussing the meaning of data, weighing the importance of different sources, pondering the possible model solutions, and making sense of output.

Every once in a while the collaboration takes place at sea! Here are some nice images of data scientist Jurie “Jannes” Germishuys from Combine AB and marine biologist Matthias Obst from SeAnalytics AB, during a recent field trip in Kosterhavets National Park. Here they dropped several remotely operated vehicles (so-called ROVs) and filmed local seafloor habitats. This way data scientists get introduced to the beauty of our marine habitats, but also to the practical work of marine scientists and the challenges associated with ocean conservation. Once we all have the same background, the technical discussions on the data management and analysis become much more meaningful.

Subsea video from an ROV in the Koster National Park. Video: Vera Lisell.

Every data point in our ODF AI models has an interesting backstory that we as data scientists don’t often know in its entirety. Interacting with domain experts during the data collection and data interpretation stages allows us to fill these important gaps in our understanding and deliver more relevant insights.

Jurie "Jannes" Germishuys Data scientist, Combine AB

We are now in a position to collect new seafloor imagery in the morning and analyze them while we’re eating lunch!

Matthias Obst Marine biologist, SeAnalytics AB

Oh, and here are three more answers to what has made ODF a success:

We have a lot of fun;
We are many partners, yielding a large pool of expertise and resources;
Our work always starts with real world challenges.

Sometimes a collaboration between marine researchers and data scientists develops into a long-term activity inspired by a common problem or interest!

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ODF Sweden will host guest professor in “Marine Citizen Science for sustainable development”

Torsten Linders — Fri, 11 Jun 2021 06:40:54 +0000

Last week came the fantastic news, that the University of Gothenburg’s vice-chancellor has appointed Dr. Uta Wehn as the Adlerbertska Research Foundation guest professor in sustainable development. ODF Sweden nominated Uta, and we were able to show a very broad and cross-disciplinary support for her nomination. We proudly welcome Uta to Sweden and to ODF. Uta will formally be hosted by the Department of Marine Sciences at University of Gothenburg.

Image: Ground Truth 2.0 (www.gt20.eu)

Sensor on fishing gear, Aleutian Islands, Alaska. Image: Lynn Selboe.

Students in the LiMPETS Monitoring program. Photo: Jessie Altstatt/NOAA

Fishery and oceanography, Greenland. Image: Uummannaq Polar Institute

Spices recognition using AI, developed by citizen science. Video: GU - Koster Seafloor Observatory

Uta’s arrival consolidates and strengthens our ambitions in citizen science. In ODF Sweden we are delighted to see that openness and inclusiveness are getting increased attention and appreciation at all levels in marine science and marine management. This spells well for more high quality ocean data, better and broader analysis and interpretation of that data, and for deeper and wider knowledge about our common oceans.

Expect great things, and join the movement! For example by sending a message to Uta and ODF Sweden. Click either of the buttons below:

This is a wonderful opportunity. First on my to-do-list is creating a lively 'community of practice' for marine citizen science. This will build on the substantial hands on experience I have gained over the years, not least in the projects Ground Truth 2.0 and CSEOL that I led as well as in MICS, WeSenseIt and WeObserve.

Uta Wehn Adlerbert Guest Professor
Associate Professor of Water Innovation Studies

Uta's arrival in Sweden will really give a push to open up how we think about marine science. Who is it for and who can contribute? These are important questions if we are serious about sustainable growth in the blue economy.

Robin teigland Director of ODF Sweden
Professor of Strategy and Management of Digitalization

Yesss! Uta's appointment is another step towards realizing of the full potential of inclusive and open ocean science in Sweden. We feel passionately about this and we have seen the payback it creates for ocean literacy and marine conservation, for example in the Koster Seafloor Observatory Welcome to ODF, Uta!

Matthias Obst Chair of Swedish Biodiversity Data Infrastructure
Associate Professor of Marine Ecology

I know the fantastic work Uta does in citizen science. This is why I suggested her name when we in ODF discussed the possibility of nominating someone for this position. I am very much looking forward to working with Uta.

Marisa Ponti Associate Professor of Informatics

This will be great, there are much synergies with what we do in ARCS. I will work together with Uta, setting up a 'community of practice', gathering people involved in marine citizen science.

Dick Kasperowski Project leader for ARCS - ARenas for Cooperation through citizen Science
Professor of Theory of Science

The Centre for Sea and Society has a mission to initiate, stimulate and develop ocean related transdisciplinary research and education. We will support Uta in all her activities. The timing is excellent, now that Sweden is gearing up its contribution to the UN Decade of Ocean Science for Sustainable Development.

Lena Gipperth Director of Centre for Sea and Society
Professor of Environmental Law

More cross-disciplinary research and practice about the relation between lay and expert knowledge is very important in marine and fisheries management. I warmly welcome Uta to Sweden and I look forward to collaboration, strengthening a holistic perspective on (marine) sustainable development.

Sebastian Linke Associate Proffessor of Environmental Social Science

Cross-disciplinary research in the maritime sector has a long tradition at the School of Business, Economics and Law. We warmly welcome Uta and look forward to collaboration.

Marie Stenseke Deputy Dean at the School of Business, Economics and Law
Professor of Human Geography

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We want to hear from you: ODF Sweden’s participant survey

Torsten Linders — Wed, 19 May 2021 13:53:00 +0000

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