Staff

GEOMAR I Helmholtz Centre for Ocean Research Kiel

Dr. Timm Schoening

Research Devision 2: Marine Biogeochemistry
Research Unit Marine Geosystems
Working Group DeepSea Monitoring

Office:
Room: 8A-210
Phone: +49 431 600-2320
Email: tschoening(at)geomar.de

Address:
Wischhofstraße 1-3
D-24148 Kiel

Research & Education

2019 - 2021 PostDoc at the GEOMAR Helmholtz-Centre for Ocean Research Kiel
in the DeepSea Monitoring Group (Prof. Dr. Jens Greinert, Marine Geosystems). Automated Image Analysis in the framework of the JPIOceans “Mining Impact 2” Project.

2018 - 2019 PostDoc in the Future Ocean excellence cluster
at the GEOMAR Helmholtz-Centre for Ocean Research Kiel.

Rapid off-shore Analysis of Marine Imagery

2018 PostDoc at Okeanos, University of the Azores, Horta, Portugal
(DFG Research Fellowship).
Exploiting 3D information for an automated semantic analysis of underwater images

2015 - 2017 PostDoc at the GEOMAR Helmholtz-Centre for Ocean Research Kiel
in the DeepSea Monitoring Group (Prof. Dr. Jens Greinert, Marine Geosystems). Automated Image Analysis in the framework of the JPIOceans “EcoMining” Project.

2015 Ph.D. in Computer Science:
"Automated detection in benthic images for megafauna classification and marine resource exploration: supervised and unsupervised methods for classification and regression tasks in benthic images with efficient integration of expert knowledge" (Bielefeld University)

2010 M.Sc. in Computer Science in the Natural Sciences:
"Towards Improved Epilepsia Diagnosis by Unsupervised Segmentation of Neuropathology Tissue Sections using Ripley's-L Features" (Bielefeld University)

2008 B.Sc. in Computer Science in the Natural Sciences:
"Web 2.0 techniques for exploratory image database analysis" (Bielefeld University)

 

Practical Experience

 

Co-host of the 2019 “Image Analysis Days Schleswig-Holstein”

Chair of the scientific and local organizing committees to conduct the second Marine Imaging Workshop (held in February 2017 at GEOMAR)

Co-chair of the scientific organizing committee that initiated and conducted the first Marine Imaging Workshop (held in April 2014 at the National Oceanographic Centre, UK) with three days of poster and technical presentations of 100 international participants.

Exchange semester to visit the Bioimage Analysis Lab at the University of Warwick, UK

Prizes

Briese Research PhD Award for Marine Science


Grants

iAtlantic Project Co-Proponent (EU H2020)

Exploiting 3D information for an automated semantic analysis of underwater images” (DFG Research Fellowship)

Rapid, offshore Analysis of Marine Imagery” (Future Ocean Excellence Cluster – PostDoc Project Call)

General Purpose Underwater Spectral Imaging” (Future Ocean Excellence Cluster – Investment Call, proposal supporter)

Multi-Spectral Image Capture” (GEOMAR Seed Funding)


Cruises

RV Sonne SO268-1&2: Manzanillo – Vancouver; Station Planning, AUV Operations, Optical and Sensor Network Data Management, Automated Image Analysis, Manganese Nodule Measurements from BoxCores, Deployment Management in GIS

PI for RV Poseidon cruise POS526 “SeaSOM”: Bergen – Kiel; Semi-autonomous optical monitoring technologies for bubble release sites and cold water coral reefs

MIDAS Pelagia cruise: Faial – Faial; ROV and towed camera operations, data management and imagery analysis

RV Sonne SO242-1: Guayaquil – Guayaquil; AUV operation, image analysis and annotation

RV Sonne SO239: Panama – Manzanillo; AUV operation, image analysis and annotation

RV Sonne Testcruise: Kiel – Gran Canaria; ROV video analysis and annotation

 

 

Research interests

My work aims to monitor the deep-sea with methods of pattern recognition and image processing. The focus lies on the exploration of large archives of 2D and 3D images of benthic and pelagic images.

Monitoring poly-metallic nodule abundance

In cooperation with the JPIO Partners, BGR and Saltation Marine IT, the amount, size and finally mass of polymetallic nodules lying on the seafloor is to be estimated. To monitor the minerals as well as the diverse biology in this sensitive habitat, precise measurements are required. This includes detections of the nodules as well as the biology.

The first part of this project was targeted to derive the percentage of the seafloor covered in nodules. Subsequently more detailed segmentation yielded single nodule sizes, and, combined with automatically detected laser markers, the relative size of the nodules in cm.

Automated detection of benthic mega fauna

One of the major projects, is the automated detection of mega fauna (as well as flora and Lebensspuren created by those animals). Images are provided by collaboration partners at the Alfred Wegener Institute and NOC Southampton. One result is an automated detection system (called iSIS, intelligent screening of image series) that incorporates the expertise of the biologists while keeping their input as small as possible. Parameters for different steps of the system are derived from a fully-annotated workshop transect. As the central part, supervised machine-learning is applied by Support Vector Machines.

Manual image annotation

A basis for the application of supervised and semi-supervised machine learning algorithms is a training set of reference samples. To obtain such a reference set, image annotation is required which was facilitated in different ways. Initially, whole images can be annotated using BIIGLE. More features and efficiency is currently implemented for the successor DIAS (Discol Image Annotation System) being developed for the JPIO Mining Impact project.

Web based visualization tools

A wide range of research focused visualizations tools has been implemented. These mostly facilitate link and brush interfaces to fuse representations of complex feature based descriptions with images or plots.

Selected Publications

Peer Reviewed

Timm Schoening, Kevin Köser, Jens Greinert. An acquisition, curation and management workflow for sustainable, terabyte-scale marine image analysis. Scientific Data

https://doi.org/10.1038/sdata.2018.181

Hongbo Liu, Jan Sticklus, Kevin Köser, Henk-Jan Hoving, Hong Song, Ying Chen, Jens Greinert, Timm Schoening. TuLUMIS - A tunable LED-based underwater multispectral imaging system. Optics Express

Alevizos, E., Schoening, T., Köser, K., Snellen, M., & Greinert, J. Quantification of the fine-scale distribution of Mn-nodules: insights from AUV multi-beam and optical imagery data fusion. Biogeosciences Discussions, 1-29.

Peukert, A., Schoening, T., Alevizos, E., Köser, K., Kwasnitschka, T., & Greinert, J. Understanding Mn-nodule distribution and related deep-sea mining impacts using AUV-based hydroacoustic sensing and optical observations. Biogeosciences Discussions, 1-33.

Timm Schoening, Daniel Jones, Jens Greinert Compact Morphology based Delineation of Poly-Metallic Nodules (Nature Scientific Reports)

https://doi.org/10.1038/s41598-017-13335-x

Daniel Langenkämper, Martin Zurowietz, Timm Schoening, Tim W. Nattkemper BIIGLE 2.0 - Browsing and Annotating Large Marine Image Collections (Frontiers in Marine Science)

https://doi.org/10.3389/fmars.2017.00083

Jose Nuno Gomes Pereira et al. Current and Future Trends in Marine Image Annotation Software (Progress in Oceanography)

https://doi.org/10.1016/j.pocean.2016.07.005

Timm Schoening, Thomas Kuhn, Daniel OB Jones, Erik Simon-Lledo, Tim W Nattkemper Fully automated image segmentation for benthic resource assessment of poly-metallic nodules (Methods in Oceanography)

https://doi.org/10.1016/j.mio.2016.04.002

Timm Schoening, Jonas Osterloff, Tim W Nattkemper RecoMIA - Recommendations for Marine Image Annotation: Lessons Learned and Future Directions (Frontiers in Marine Science)

https://doi.org/10.3389/fmars.2016.00059

Tom Kwasnitschka, Kevin Köser, Jan Sticklus, Marcel Rothenbeck, Tim Weiß, Emanuel Wenzlaff, Timm Schoening, Lars Triebe, Anja Steinführer, Colin Devey, Jens Greinert DeepSurveyCam - A Deep Ocean Optical Mapping System (Sensors)

http://dx.doi.org/10.3390/s16020164

Jennifer M Durden, Brian J Bett, Timm Schoening, Kirsty J Morris, Tim W Nattkemper, Henry A Ruhl Comparison of image annotation data generated by multiple investigators for benthic ecology (Marine Ecology Progress Series)

http://dx.doi.org/10.3354/meps11775

Timm Schoening, Thomas Kuhn, Melanie Bergmann, Tim W Nattkemper DELPHI - fast and adaptive computational laser point detection and visual footprint quantification for arbitrary underwater image collections (Frontiers in Marine Science)

https://doi.org/10.3389/fmars.2015.00020

Timm Schoening, Thomas Kuhn, Tim W Nattkemper Seabed classification using a bag-of-prototypes feature representation (International Conference on Pattern Recognition)

https://doi.org/10.1109/CVAUI.2014.9

Tim W Nattkemper, Timm Schoening, Daniel Brün Image-based Marine Resource Exploration and Biodiversity Assessment with MAMAS (Marine data Asset Management and Analysis System) (Underwater Mining Institute)

Timm Schoening, Björn Steinbrink, Daniel Brün, Thomas Kuhn, Tim W Nattkemper Ultra-fast segmentation and quantification of poly-metallic nodule coverage in high resolution digital images (Underwater Mining Institute)

Autun Purser, Jörg Ontrup, Timm Schoening, Laurenz Thomsen, Tim W Nattkemper Microhabitat and shrimp abundance within a Norwegian cold-water coral ecosystem (Biogeosciences)

https://doi.org/10.5194/bg-10-5779-2013

Timm Schoening, Melanie Bergmann, Tim W. Nattkemper Investigation of hidden parameters influencing the automated object detection in images from the deep seafloor of the HAUSGARTEN observatory (OCEANS)

Timm Schoening, Thomas Kuhn, Tim W. Nattkemper Estimation of poly-metallic nodule coverage in benthic images (Underwater Mining Institute)

Timm Schoening, Melanie Bergmann, Jörg Ontrup, et al. Semi-Automated Image Analysis for the Assessment of Megafaunal Densities at the Arctic Deep-Sea Observatory HAUSGARTEN (PLoS ONE)

https://doi.org/10.1371/journal.pone.0038179

Timm Schoening, Volkmar Hans, Tim W. Nattkemper Towards improved epilepsia diagnosis by unsupervised segmentation of neuropathological tissue sections using Ripley's-L features (Bildverarbeitung für die Medizin)

Timm Schoening, Nils Ehnert, Jörg Ontrup, Tim W. Nattkemper

Biigle Tools – A Web 2.0 approach for Visual Bioimage Database Mining (Information Visualization)


Data Publications 

Schoening, Timm; Gazis, Iason-Zois (2019): Summary of sizes, weights, counts and coverage of poly-metallic nodules from box cores taken during SONNE cruises SO268/1 and SO268/2. https://doi.pangaea.de/10.1594/PANGAEA.904967

Schoening, Timm; Gazis, Iason-Zois (2019): Sizes, weights and volumes of poly-metallic nodules from box cores taken during SONNE cruises SO268/1 and SO268/2. https://doi.pangaea.de/10.1594/PANGAEA.904962

Schoening, Timm (2017): Results of nodule detection along AUV tracks during SONNE cruises SO239 and SO242/1. https://doi.pangaea.de/10.1594/PANGAEA.883838

Greinert, Jens; Weiß, Tim; Schoening, Timm (2018): Raw data from Miniature Autonomous Plume recorder (MAPR) at stations during SONNE cruise SO242/2. https://doi.pangaea.de/10.1594/PANGAEA.892740

Greinert, Jens; Weiß, Tim; Schoening, Timm (2018): Raw data from Miniature Autonomous Plume recorder (MAPR) at stations during SONNE cruise SO242/1. https://doi.pangaea.de/10.1594/PANGAEA.886533

Greinert, Jens; Weiß, Tim; Schoening, Timm (2018): Raw data from Miniature Autonomous Plume recorder (MAPR) at stations during SONNE cruise SO239. https://doi.pangaea.de/10.1594/PANGAEA.886182

Schoening, Timm (2017): Source code for the Compact Morphology-based Nodule Delineation (CoMoNoD) algorithm. https://doi.org/10.1594/PANGAEA.875070

Greinert, Jens; Schoening, Timm; Köser, Kevin; Rothenbeck, Marcel (2017): Seafloor images and raw context data along AUV tracks during SONNE cruises SO239 and SO242/1. https://doi.org/10.1594/PANGAEA.882349

Schoening, Timm; Schütt, Andrea (2017): Simulated Hierarchical Benchmark Dataset to assess dendro-classification methods (hierarchical classification). https://doi.org/10.1594/PANGAEA.884173

Other Publications

Timm Schoening et al. „Report on the Marine Imaging Workshop 2017” (Research Ideas and Outcomes)

https://doi.org/10.3897/rio.3.e13820

Ian Stewart et al. MIDAS Deliverable 10.5: “Report on the appropriateness of the testing of the protocols and standards developed in WP8”

Jen Durden, Timm Schoening et al. Visual imaging for marine biological and ecological research (Oceanography and Marine Biology: An Annual Review)

Ann Vanreusel et al. MIDAS Deliverable 10.4: “Tools for Rapid Biodiversity Assessment”

JPIO “Ecological Aspects of Deep-Sea Mining” Progress Report 2015 – Section Work Package 1

Jens Greinert et al. “RV Sonne Cruise Report SO242-1” http://dx.doi.org/10.3289/GEOMAR_REP_NS_26_2015

Lenaick Menot et al. MIDAS Deliverable 10.2: “Integrative Habitat Mapping Technologies”

Pedro Martinez Arbizu et al. “RV Sonne Cruise Report SO239”

http://dx.doi.org/10.3289/GEOMAR_REP_NS_25_2015

Jan Schulz et al. Aquatische Optische Technologien (Marine Science Reports)