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Fish embryo models are increasingly being used both for the assessment of chemicals efficacy and potential toxicity. This article proposes a methodology to automatically detect the swim bladder on 2D images of Medaka fish embryos seen…
Marine ecosystems are in the spotlight, because environmental changes are threatening biodiversity and ecological functions. In this context, microalgae play key ecological roles both in planktonic and benthic ecosystems. Consequently, they…
The advances of next-generation sequencing technology have accelerated study of the microbiome and stimulated the high throughput profiling of metagenomes. The large volume of sequenced data has encouraged the rise of various studies for…
We present a computational live bacteria detection system that periodically captures coherent microscopy images of bacterial growth inside a 60 mm diameter agar-plate and analyzes these time-lapsed holograms using deep neural networks for…
The ability to estimate invertebrate biomass using only images could help scaling up quantitative biodiversity monitoring efforts. Computer vision-based methods have the potential to omit the manual, time-consuming, and destructive process…
Cultivating oleaginous microalgae in specific culturing devices such as raceways is seen as a future way to produce biofuel. The complexity of this process coupling non linear biological activity to hydrodynamics makes the optimization…
Manual determination of plant phenotypic properties such as plant architecture, growth, and health is very time consuming and sometimes destructive. Automatic image analysis has become a popular approach. This research aims to identify the…
Metagenomics has lowered the barrier to microbial discovery--enabling the identification of novel microbes without isolation--but cultures remain imperative for the deep study of microbes. Cultivation and isolation of non-model microbes…
Food crystal agglomeration is a phenomenon occurs during crystallization which traps water between crystals and affects food product quality. Manual annotation of agglomeration in 2D microscopic images is particularly difficult due to the…
In this work we present a device specifically designed to study microbial growth with several applications related to environmental microbiology and other areas of research as astrobiology. The Automated Measuring and Cultivation device…
Interactions between bacteria and protozoa is an increasing area of interest, however there are a few systems that allow extensive observation of the interactions. We examined a surface system consisting of non nutrient agar with a uniform…
Mycelium is a promising biomaterial based on fungal mycelium, a highly porous, nanofibrous structure. Scanning electron micrographs are used to characterize its network, but the currently available tools for nanofibrous microstructures do…
As for many motile micro-algae, the freshwater species Chlamydomonas reinhardtii can detect light sources and adapt its motile behavior in response. Here, we show that suspensions of photophobic cells can be unstable to density…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
With the acceleration of urbanization and living standards, microorganisms play increasingly important roles in industrial production, bio-technique, and food safety testing. Microorganism biovolume measurements are one of the essential…
Mussel platforms are big floating structures made of wood (size is normally about 20x20 meters or even a bit larger) that are used for aquaculture, id EST: growing mussels in appropriate marine waters. These structures are very typical in…
One of the major research questions regarding human microbiome studies is the feasibility of designing interventions that modulate the composition of the microbiome to promote health and cure disease. This requires extensive understanding…
Chromosome analysis and identification from metaphase images is a critical part of cytogenetics based medical diagnosis. It is mainly used for identifying constitutional, prenatal and acquired abnormalities in the diagnosis of genetic…
Climate change is increasing the frequency and severity of harmful algal blooms (HABs), which cause significant fish deaths in aquaculture farms. This contributes to ocean pollution and greenhouse gas (GHG) emissions since dead fish are…
Industrial mushroom cultivation increasingly relies on computer vision for monitoring and automated harvesting. However, developing accurate detection and segmentation models requires large, precisely annotated datasets that are costly to…