| 1. |
- Midtvedt, Benjamin, et al.
(författare)
-
Single-shot self-supervised object detection in microscopy
- 2022
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723 .- 2041-1723. ; 13:1
-
Tidskriftsartikel (refereegranskat)abstract
- Object detection is a fundamental task in digital microscopy, where machine learning has made great strides in overcoming the limitations of classical approaches. The training of state-of-the-art machine-learning methods almost universally relies on vast amounts of labeled experimental data or the ability to numerically simulate realistic datasets. However, experimental data are often challenging to label and cannot be easily reproduced numerically. Here, we propose a deep-learning method, named LodeSTAR (Localization and detection from Symmetries, Translations And Rotations), that learns to detect microscopic objects with sub-pixel accuracy from a single unlabeled experimental image by exploiting the inherent roto-translational symmetries of this task. We demonstrate that LodeSTAR outperforms traditional methods in terms of accuracy, also when analyzing challenging experimental data containing densely packed cells or noisy backgrounds. Furthermore, by exploiting additional symmetries we show that LodeSTAR can measure other properties, e.g., vertical position and polarizability in holographic microscopy.
|
|
| 2. |
- Arias, A., et al.
(författare)
-
Predator Chemical Cue Effects on the Diel Feeding Behaviour of Marine Protists
- 2021
-
Ingår i: Microbial Ecology. - : Springer Science and Business Media LLC. - 0095-3628 .- 1432-184X. ; 82:2, s. 356-364
-
Tidskriftsartikel (refereegranskat)abstract
- We have assessed the effect of copepod chemical cues on the diel feeding rhythms of heterotrophic and mixotrophic marine protists. All phagotrophic protists studied exhibited relatively high diurnal feeding rates. The magnitude of the diel feeding rhythm, expressed as the quotient of day and night ingestion rates, was inversely related to the time that phagotrophic protists were maintained in the laboratory in an environment without predators. In the case of the recently isolated ciliate Strombidium arenicola, the rhythm was lost after a few months. When challenged with chemical alarm signals (copepodamides) from the copepod Calanus finmarchicus at realistic concentrations (0.6-6 pM), S. arenicola partially re-established diurnal feeding. Conversely, the amplitude of the diel feeding rhythm for the ciliate Mesodinium rubrum was not affected by copepodamides, although the 24-h integrated food intake increased by approximately 23%. For the dinoflagellates Gyrodinium dominans and Karlodinium armiger, copepodamides significantly reduced the amplitude of their diel feeding rhythms; significant positive effects on total daily ingestion were only observed in G. dominans. Finally, the dinoflagellate Oxyrrhis marina, isolated >20 years ago, showed inconsistent responses to copepodamides, except for an average 6% increase in its total ingestion over 24 h. Our results demonstrate that the predation risk by copepods affects the diel feeding rhythm of marine protists and suggests a species-specific response to predation threats.
|
|
| 3. |
- Bachimanchi, Harshith, et al.
(författare)
-
Deep-learning-powered data analysis in plankton ecology
- 2024
-
Ingår i: Limnology And Oceanography Letters. - 2378-2242.
-
Forskningsöversikt (refereegranskat)abstract
- The implementation of deep learning algorithms has brought new perspectives to plankton ecology. Emerging as an alternative approach to established methods, deep learning offers objective schemes to investigate plankton organisms in diverse environments. We provide an overview of deep-learning-based methods including detection and classification of phytoplankton and zooplankton images, foraging and swimming behavior analysis, and finally ecological modeling. Deep learning has the potential to speed up the analysis and reduce the human experimental bias, thus enabling data acquisition at relevant temporal and spatial scales with improved reproducibility. We also discuss shortcomings and show how deep learning architectures have evolved to mitigate imprecise readouts. Finally, we suggest opportunities where deep learning is particularly likely to catalyze plankton research. The examples are accompanied by detailed tutorials and code samples that allow readers to apply the methods described in this review to their own data.
|
|
| 4. |
- Bachimanchi, Harshith, et al.
(författare)
-
Microplankton life histories revealed by holographic microscopy and deep learning
- 2022
-
Ingår i: eLife. - 2050-084X. ; 11
-
Tidskriftsartikel (refereegranskat)abstract
- The marine microbial food web plays a central role in the global carbon cycle. However, our mechanistic understanding of the ocean is biased toward its larger constituents, while rates and biomass fluxes in the microbial food web are mainly inferred from indirect measurements and ensemble averages. Yet, resolution at the level of the individual microplankton is required to advance our understanding of the microbial food web. Here, we demonstrate that, by combining holographic microscopy with deep learning, we can follow microplanktons throughout their lifespan, continuously measuring their three-dimensional position and dry mass. The deep-learning algorithms circumvent the computationally intensive processing of holographic data and allow rapid measurements over extended time periods. This permits us to reliably estimate growth rates, both in terms of dry mass increase and cell divisions, as well as to measure trophic interactions between species such as predation events. The individual resolution provides information about selectivity, individual feeding rates, and handling times for individual microplanktons. The method is particularly useful to detail the rates and routes of organic matter transfer in micro-zooplankton, the most important and least known group of primary consumers in the oceans. Studying individual interactions in idealized small systems provides insights that help us understand microbial food webs and ultimately larger-scale processes. We exemplify this by detailed descriptions of micro-zooplankton feeding events, cell divisions, and long-term monitoring of single cells from division to division.
|
|
| 5. |
- Bourlat, Sarah, et al.
(författare)
-
Wrasse fishery on the Swedish West Coast: towards ecosystem-based management
- 2021
-
Ingår i: ICES Journal of Marine Science. - : Oxford University Press (OUP). - 1054-3139 .- 1095-9289. ; :fsaa249
-
Tidskriftsartikel (refereegranskat)abstract
- Fishing and translocation of marine species for use in aquaculture is widespread. Corkwing, goldsinny, and ballan wrasse (Symphodus melops, Ctenolabrus rupestris, and Labrus bergylta) are fished on the Swedish west coast for use as cleaner-fish in Norwegian salmon farms. Here, we aim to provide knowledge and recommendations to support ecosystem-based management for wrasse fisheries in Sweden. We compared fished and non-fished areas to test if current fishery levels have led to stock depletion. To gain insight on the role of wrasse in the algal belt trophic chain, we analysed the gut contents of goldsinny and corkwing using metabarcoding. Finally, we analysed the trophic interactions of wrasse and potential prey in a mesocosm study. We could not detect any signs of stock depletion or altered size structure in fished areas compared to the protected control area. Gut analyses confirmed both goldsinny and corkwing as non-specialized, omnivorous opportunists and revealed, with 189 prey taxa detected, a broader spectrum of prey than previously known. Common prey items included mesoherbivores such as small gastropods and crustaceans, but also insects and algae. We conclude that there are no visible signs of stock depletion at the current removal level of wrasses by the fishery. However, this emerging fishery should be closely monitored for potential cascading effects on the algal belt ecosystem, and our study could provide a baseline for future monitoring.
|
|
| 6. |
- Rigby, Kristie, 1987, et al.
(författare)
-
Predatory cues drive colony size reduction in marine diatoms
- 2021
-
Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 11:16, s. 11020-11027
-
Tidskriftsartikel (refereegranskat)abstract
- Colony formation is a common feature among nonmotile marine phytoplankton. Several theories exist around the potential benefits of larger colonies. Here, we test the hypothesis that predation is one of the drivers behind colony formation and chain length plasticity. We exposed cultures of Thalassiosira rotula, Chaetoceros curvisetus, and Chaetoceros affinis to copepodamides, a chemical alarm cue released by copepods and perceived as an indicator of predation threat by their prey. This was coupled with a grazing experiment, which compared copepod grazing rates on different chain lengths. Our results show that T. rotula and C. curvisetus decreased their chain lengths by 79% and 49%, respectively, in response to copepodamides. Single cells and short chains were grazed at lower rates compared with long chains, and the copepodamide-driven size shift led to 30% and 12% lower grazing in T. rotula and C. curvisetus, respectively. In contrast, C. affinis showed a slight increased chain length in response to copepodamides although nonsignificant. We found that 2 of 3 studied species reduce their chain length in response to the presence of copepod grazers. Altered size structure has implications for the route of carbon in the marine food webs and carbon export to deeper strata.
|
|
| 7. |
- Rigby, Kristie, 1987, et al.
(författare)
-
Species Specific Responses to Grazer Cues and Acidification in Phytoplankton- Winners and Losers in a Changing World
- 2022
-
Ingår i: Frontiers in Marine Sceince. - : Frontiers Media SA. - 2296-7745. ; 9
-
Tidskriftsartikel (refereegranskat)abstract
- Phytoplankton induce defensive traits in response to chemical alarm signals from grazing zooplankton. However, these signals are potentially vulnerable to changes in pH and it is not yet known how predator recognition may be affected by ocean acidification. We exposed four species of diatoms and one toxic dinoflagellate to futurepCO2levels, projected by the turn of the century, in factorial combinations with predatory cues from copepods (copepodamides). We measured the change in growth, chain length, silica content, and toxin content. Effects of increasedpCO2were highly species specific. The induction of defensive traits was accompanied by a significant reduction in growth rate in three out of five species. The reduction averaged 39% and we interpret this as an allocation cost associated with defensive traits. Copepodamides induced significant chain length reduction in three of the four diatom species. Under elevatedpCO2Skeletonema marinoireduced silica content by 30% and inAlexandrium minutumthe toxin content was reduced by 30%. Using copepodamides to induce defensive traits in the absence of direct grazing provides a straightforward methodology to assess costs of defense in microplankton. We conclude that copepodamide signalling system is likely robust to ocean acidification. Moreover, the variable responses of different taxa to ocean acidification suggest that there will be winners and losers in a highpCO2world, and that ocean acidification may have structuring effects on phytoplankton communities.
|
|
| 8. |
- Robinson, N. A., et al.
(författare)
-
Applying genetic technologies to combat infectious diseases in aquaculture
- 2022
-
Ingår i: Reviews in Aquaculture. - : Wiley. - 1753-5123 .- 1753-5131. ; 15:2, s. 491-535
-
Tidskriftsartikel (refereegranskat)abstract
- Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies—sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture. © 2022 The Authors. Reviews in Aquaculture published by John Wiley & Sons Australia, Ltd.
|
|
| 9. |
- Ryderheim, F., et al.
(författare)
-
Predator-induced defence in a dinoflagellate generates benefits without direct costs
- 2021
-
Ingår i: Isme Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 15, s. 2107-2116
-
Tidskriftsartikel (refereegranskat)abstract
- Inducible defences in phytoplankton are often assumed to come at a cost to the organism, but trade-offs have proven hard to establish experimentally. A reason for this may be that some trade-off costs only become evident under resource-limiting conditions. To explore the effect of nutrient limitation on trade-offs in toxin-producing dinoflagellates, we induced toxin production in Alexandrium minutum by chemical cues from copepods under different levels of nitrogen limitation. The effects were both nitrogen- and grazer-concentration dependent. Induced cells had higher cellular toxin content and a larger fraction of the cells was rejected by a copepod, demonstrating the clear benefits of toxin production. Induced cells also had a higher carbon and nitrogen content, despite up to 25% reduction in cell size. Unexpectedly, induced cells seemed to grow faster than controls, likely owing to a higher specific nutrient affinity due to reduced size. We thus found no clear trade-offs, rather the opposite. However, indirect ecological costs that do not manifest under laboratory conditions may be important. Inducing appropriate defence traits in response to threat-specific warning signals may also prevent larger cumulative costs from expressing several defensive traits simultaneously.
|
|
| 10. |
- Selander, Erik, 1973, et al.
(författare)
-
Chemical signaling in the turbulent ocean-hide and seek at the Kolmogorov scale
- 2020
-
Ingår i: Fluids. - : MDPI AG. - 2311-5521. ; 5:2
-
Tidskriftsartikel (refereegranskat)abstract
- Chemical cues and signals mediate resource acquisition, mate finding, and the assessment of predation risk in marine plankton. Here, we use the chemical properties of the first identified chemical cues from zooplankton together with in situ measurements of turbulent dissipation rates to calculate the effect of turbulence on the distribution of cues behind swimmers as well as steady state background concentrations in surrounding water. We further show that common zooplankton (copepods) appears to optimize mate finding by aggregating at the surface in calm conditions when turbulence do not prevent trail following. This near surface environment is characterized by anisotropic turbulence and we show, using direct numerical simulations, that chemical cues distribute more in the horizontal plane than vertically in these conditions. Zooplankton may consequently benefit from adopting specific search strategies near the surface as well as in strong stratification where similar flow fields develop. Steady state concentrations, where exudation is balanced by degradation develops in a time scale of ~5 h. We conclude that the trails behind millimeter-sized copepods can be detected in naturally occurring turbulence below the wind mixed surface layer or in the absence of strong wind. The trails, however, shorten dramatically at high turbulent dissipation rates, above ~10−3 cm2 s−3 (10−7 W kg−1). © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
|
|
