A5057316063- Diatoms and Algae Research
- Marine and coastal ecosystems
- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Radioactivity and Radon Measurements
- Radioactive contamination and transfer
- Aquatic Ecosystems and Phytoplankton Dynamics
- Freshwater macroinvertebrate diversity and ecology
- Marine Biology and Ecology Research
- Geology and Paleoclimatology Research
- Spectroscopy Techniques in Biomedical and Chemical Research
- Bacteriophages and microbial interactions
- Identification and Quantification in Food
- Water Quality Monitoring Technologies
- Species Distribution and Climate Change
- Photoacoustic and Ultrasonic Imaging
- Advanced Fluorescence Microscopy Techniques
- Data Mining Algorithms and Applications
- Algal biology and biofuel production
- Evolution and Paleontology Studies
- Topic Modeling
- Geochemistry and Geologic Mapping
- Water Quality Monitoring and Analysis
- Advanced Text Analysis Techniques
- Bacillus and Francisella bacterial research
University of Duisburg-Essen
2020-2024
University of Applied Sciences Emden Leer
2010-2019
Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung
2014-2019
Senatsverwaltung für Stadtentwicklung und Wohnen
2007-2015
Senatsverwaltung für Gesundheit, Pflege und Gleichstellung
2010-2011
Light microscopic analysis of diatom frustules is widely used both in basic and applied research, notably taxonomy, morphometrics, water quality monitoring paleo-environmental studies. In these applications, usually large numbers need to be identified and/or measured. Although there a for automation image processing methods supporting tasks have previously been developed, they did not become widespread analysis. While methodological reports wide variety segmentation, identification feature...
Abstract Deep convolutional neural networks are emerging as the state of art method for supervised classification images also in context taxonomic identification. Different morphologies and imaging technologies applied across organismal groups lead to highly specific image domains, which need customization deep learning solutions. Here we provide an example using (CNNs) identification morphologically diverse microalgal group diatoms. Using a combination high-resolution slide scanning...
Field observations form the basis of majority studies on microphytobenthic algal communities in freshwater ecosystems. Controlled mesocosm experiments data are comparatively uncommon. The few experimental that have been conducted provide valuable insights into how multiple stressors affect community structures and photosynthesis-related traits benthic microalgae. recovery process after subsided, however, has received less attention studies. To close this gap, here we present results a...
Light microscopy analysis of diatom frustules is widely used in basic and applied research, notably taxonomy, morphometrics, water quality monitoring paleo-environmental studies. Although there a need for automation these applications, various developments image processing methodology supporting tasks have not become widespread diatom-based analyses. We addressed this issue by combining our automated software SHERPA with commercial slide-scanning microscope. The resulting workflow enables...
Fragilariopsis kerguelensis is one of the most abundant diatoms in sediments Southern Ocean. Its morphometric features have been proposed as proxies, based on links with, for example, iron availability, sea surface temperature and glacial/interglacial conditions. We investigated changes F. valves a well-studied sediment core record, focusing transition periods between glacials interglacials. By applying high-throughput diatom imaging morphometry workflow, we found two clearly distinct...
Diatom identification and counting by light microscopy of permanently embedded acid-cleaned silicate shells (frustules) is a fundamental method in ecological water quality investigations. Here we present new variant this based on “digital virtual slides”, compare it to the traditional, non-digitized workflow freshwater samples. We analysed three replicate slides taken from six benthic samples using two methods: (1) working directly microscope (the “traditional” method), (2) preparing...
The marine waters around the South Shetland Islands are paramount in primary production of this Antarctic ecosystem. With increasing effects climate change and annual retreat ice shelf, importance macroalgae their diatom epiphytes also increases. relationships interactions between these organisms have scarcely been studied Antarctica, even less volcanic ecosystem Deception Island, which can be seen as a natural proxy Antarctica because its vulcanism, open system Livingston Island. In study...
Semiautomated methods for microscopic image acquisition, analysis, and taxonomic identification have repeatedly received attention in diatom analysis. Less well studied is the question whether how such might prove useful clarifying delimitation of species that are difficult to separate human taxonomists. To try answer this question, three very similar Fragilariopsis endemic Southern Ocean were targeted study: F. obliquecostata , ritscheri sublinearis . A set 501 extended focus depth specimen...
Diatoms represent one of the morphologically and taxonomically most diverse groups microscopic eukaryotes. Light microscopy-based taxonomic identification enumeration frustules, silica shells these microalgae, is broadly used in aquatic ecology biomonitoring. One key step emerging digital variants such investigations segmentation, a task that has been addressed before, but usually manually captured megapixel-sized images individual diatom cells with mostly clean background. In this paper, we...
Abstract Background Diatoms are microalgae with finely ornamented microscopic silica shells. Their taxonomic identification by light microscopy is routinely used as part of community ecological research well status assessment aquatic ecosystems, and a need for digitalization these methods has long been recognized. Alongside their high morphological diversity, several other factors make diatoms highly challenging deep learning–based using images. These include (i) an unusually intraclass...
Fragilariopsiskerguelensis (O' Meara) Hust. is a ubiquitous diatom of the Southern Ocean. Its thick frustules are numerically dominant component siliceous sediment layer covering large parts seafloor beneath. Morphometric variability this has been interest for paleoenvironmental reconstructions. Recently, two morphotypes differentiated by morphometric descriptor rectangularity were described from Ocean core, relative abundance which correlated with reconstructed paleotemperatures. In present...
Some aspects of the life cycle Southern Ocean diatom Fragilariopsis kerguelensis have been investigated previously, but many its details not surveyed in nature. We material from a two-year sediment trap time series by high-throughput imaging and image analysis, looking for morphometric signals stages. Valve length distributions appeared close to unimodal positively (right-) skewed. Size cohorts resulting synchronized sexual reproduction events were clearly distinguishable. Nevertheless,...
Raman microspectroscopy has been used to thoroughly assess growth dynamics and heterogeneity of prokaryotic cells, yet little is known about how the chemistry individual cells changes during infection with virulent viruses, resulting in so-called virocells. Here, we investigate biochemical bacterial archaeal three different species laboratory cultures before after addition their respective viruses using single-cell microspectroscopy. By applying multivariate statistics, identified...
Diatom identification and counting by light microscopy is a fundamental method in ecological water quality investigations. Here we present new variant of this based on “digital virtual slides”, compare it to the traditional, non-digitized workflow. We analysed three replicates six samples using two methods: 1) working directly microscope (the “traditional” method), 2) preparing “virtual digital slides” high-resolution slide scanning...
It has been shown that size of planktonic diatoms responds to changes in water chemistry, but little is known about the influence different types environmental factors upon benthic diatom variation. Here we ask whether chemistry or hydromorphological influences show a stronger effect on morphometry. 10,624 valves / frustules were imaged, identified and measured from 48 samples across eight sites Ebro river basin obtained during ten years biomonitoring work. We analysed how differences...
Large lowland rivers represent an important type of ecosystem that has been under a constant anthropogenic influence (industry, thermal power plants, untreated communal water, and agriculture) for centuries, which led to most them no longer meeting natural reference conditions. These pressures affect diatom communities reliable bioindicator the overall degradation water bodies. The current study provides detailed information about benthic diatoms from large international Sava Tisa, analyzed...
Digital Micromirror Device based microscopy combines fast confocal 4D-microscopy along with conventional methods for light and new technological approaches to a versatile tool the observation of in vivo processes living biological cells measurement technical surfaces. Due use variable size pinholes adjustable scan patterns conditions can easily be optimized prerequisites sample "on fly".