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Biology subjects

Munthe-Kaas, A.

Publications and source records attributed to Munthe-Kaas, A..

2 recordsLinked to original sources

FishProx: Proximate conspecific interaction of Atlantic salmon (Salmo salar) for behavioural analysis through instance segmentation masks

In modern fish production and experimental facilities, camera installations are increasingly common for monitoring animal welfare. This opens up a new alley of autonomous tracking systems levering streamed data. However, the substantial amount of data necessitates condensation for human operators. In this paper, we present the out-of-the-box pipeline called FishProx that starts with the imagery of fish in tanks and ends in the calculation of welfare impacting factors through anomaly scores. The utilisation of the Segment Anything Model (SAM) is the basis for the identification of feeding behaviour and also (ab)normal behaviour through analysing snapshots of the fish tanks to infer metrics such as fish cohesion and cluster alignment, alongside the detection count. Our method employs automatic and robust algorithms for camera systems, making additional labelled data unnecessary, thereby saving energy and costs. Furthermore, automatic fish observation coupled with integrated analytical capabilities can lead to a sensible autonomous decision-making process. Lastly, by providing objective metrics, our approach might guide the enabling of automatic quantification of fish states, making comparative studies possible.

animal behavior and cognition↗

Perfusion estimation using MRI-based measurements and a porous media flow model

The measurement of perfusion and filtration of blood in biological tissue give rise to important clinical parameters used in diagnosis, follow-up, and therapy. In this paper we address techniques for perfusion analysis using processed contrast agent concentration data from dynamic MRI acquisitions. New methodology for analysis is evaluated and verified using synthetic data generated on a tissue geometry. Author summaryAccurate knowledge of tissue perfusion is crucial for proper diagnostics and treatment of several medical disorders. Traditional methods based on medical imaging are fast, but usually lack precision and robustness. In this paper, we address methodology to develop better diagnosis and treatment strategies for malignant tumors and stroke where blood perfusion may be altered. In our work, mathematical models for estimating perfusion are calibrated using magnetic resonance imaging (MRI) data, and more accurate representations of tissue parameters are provided. This methodology is a step towards minimal invasive and individually tailored diagnosis and treatment. We demonstrate the methodology with a twin-experiment using models of different complexity for generating data and estimating the tissue parameters. Both models are based on a mathematical description of how fluids flows in a porous medium, where the data-generating model uses higher resolution and a network representation of blood vessels than the estimating model. The calibration of unknown tissue parameters is done using a statistical framework, and the choice of methodology is motivated by applications from sub-surface reservoir characterization.

systems biology↗