Quantifying cardiac functions in model organisms like embryonic zebrafish is of high importance in small molecule screens for new therapeutic compounds. One relevant cardiac parameter is the ...fractional shortening (FS). A method for semi-automatic quantification of FS in video recordings of zebrafish embryo hearts is presented. The software provides automated visual information about the end-systolic and end-diastolic stages of the heart by displaying corresponding colored lines into a Motion-mode display. After manually marking the ventricle diameters in frames of end-systolic and end-diastolic stages, the FS is calculated. The software was evaluated by comparing the results of the determination of FS with results obtained from another established method. Correlations of 0.96 < r < 0.99 between the two methods were found indicating that the new software provides comparable results for the determination of the FS.
Small molecule high‐throughput screenings are essential for the fields of drug discovery and toxicology. Such screenings performed on whole animals are more physiologically relevant leading to more ...predictive results. However, due to challenges in automation, high costs and absence of miniaturized solutions for animal‐based experiments, high throughput screenings based on animal models are still in its infancy. Here a platform for miniaturized high throughput whole‐organism screenings is presented. The new platform is based on patterns of hydrophilic spots separated by superhydrophobic borders. The difference in wettability of spots and borders generates the effect of discontinuous dewetting and allows for formation of arrays of microdroplets that incorporate single fish embryos. Due to the flat border‐less nature of the platform, the system is compatible with single‐step collection of embryos and pipetting‐free parallel addition of chemical libraries using the “sandwiching method.” The system is miniaturized and allows for incubation of embryos in volumes as low as 5 µL. Finally, the platform realizes surface tension based immobilization of single embryos inside of each microcompartment and permits high‐throughput microscopic analysis directly on the platform. Thus, this method combines the advantages of microarrays, such as high‐throughput and simplicity, with the power of in vivo experiments.
A platform for miniaturized high‐throughput whole‐organism screenings is presented. The Droplet‐Microarray platform is based on patterns of hydrophilic spots separated by superhydrophobic regions and allows for spontaneous formation of arrays of microdroplets incorporating single zebrafish embryos. The system allows for compound screening of embryos in volumes as low as 5 µL and microscopic analysis directly on the platform.
Touch-response experimentation in zebrafish helps researchers better understand the link between genetics, drug effects, and behaviors. However, commonly manually conducted experimentation cannot ...fulfill a high-throughput screening and often delivers low accuracy and lacks reproducibility. Thus, the main aim of this work is to establish a fully automated robot-assisted experimentation system with minimal human participation to conduct the touch-response experimentation with freely swimming zebrafish larvae. Our designed system is able to undertake the role of repeated touch-response experiments at predefined specific location of the larvae in different ages and under different conditions, with high accuracy, robustness, and repeatability, and can also get comparable experimental results. The errors of the detection methods are less than 3 pixels and the offset errors of the touching points are less than 5%. Designed for high-efficiency experimentation, this system will promisingly release a great amount of the burden for the biological operators from touch-response experiments and may also have potential applications in other organisms for touch-evoked response analysis. Note to Practitioners-This article presented an automated touch-response experimentation system on zebrafish larvae, which can release a huge burden of the biological operators by achieving accurate, efficient, and repeated touch-response experiments. Manually conducted experiments are time-consuming and has low accuracy as well as difficult to do the quantification of the behaviors of the larvae. Our proposed system introduced an automated experiment pipeline and can also generate the behavior quantification of the larvae automatically, as the verification experiments confirmed. Basically, the research on the behaviors of zebrafish larvae requires large-scale data collection and analysis, so our system will play a vital role in such cases. Besides, the system can also be potentially used in other organisms, such as medaka larvae, and other related research, such as drug effects. In the current system, only one single larva was considered in each separate experiment, so our future work will be to achieve the experiments with multiple larvae in large scale for more high-throughput readouts and knowledge discovery.
We developed a simple screening system for the evaluation of neuromuscular and general toxicity in zebrafish embryos. The modular system consists of electrodynamic transducers above which tissue ...culture dishes with embryos can be placed. Multiple such loudspeaker-tissue culture dish pairs can be combined. Vibrational stimuli generated by the electrodynamic transducers induce a characteristic startle and escape response in the embryos. A belt-driven linear drive sequentially positions a camera above each loudspeaker to record the movement of the embryos. In this way, alterations to the startle response due to lethality or neuromuscular toxicity of chemical compounds can be visualized and quantified. We present an example of the workflow for chemical compound screening using this system, including the preparation of embryos and treatment solutions, operation of the recording system, and data analysis to calculate benchmark concentration values of compounds active in the assay. The modular assembly based on commercially available simple components makes this system both economical and flexibly adaptable to the needs of particular laboratory setups and screening purposes.
Over the last years, the zebrafish (Danio rerio) has become a key model organism in genetic and chemical screenings. A growing number of experiments and an expanding interest in zebrafish research ...makes it increasingly essential to automatize the distribution of embryos and larvae into standard microtiter plates or other sample holders for screening, often according to phenotypical features. Until now, such sorting processes have been carried out by manually handling the larvae and manual feature detection. Here, a prototype platform for image acquisition together with a classification software is presented. Zebrafish embryos and larvae and their features such as pigmentation are detected automatically from the image. Zebrafish of 4 different phenotypes can be classified through pattern recognition at 72 h post fertilization (hpf), allowing the software to classify an embryo into 2 distinct phenotypic classes: wild-type versus variant. The zebrafish phenotypes are classified with an accuracy of 79-99% without any user interaction. A description of the prototype platform and of the algorithms for image processing and pattern recognition is presented.
Biologische Modellorganismen wie z. B. die Eier des Zebrafischs müssen für Experimente in der Regel zunächst in
Mikrotiterplatten einsortiert werden, damit sie mikroskopiert werden können. Die ...Auswertung des dabei gewonnenen
Bildmaterials erfolgt anschließend, wie die anderen Prozessschritte auch, meist manuell. Aus diesem Grund wurden Systeme
zur Automatisierung der verschiedenen Prozessschritte am Institut für Angewandte Informatik entwickelt. Die ausgewählten
Beispiele beinhalten das automatische Sortieren von Zebrafischeiern durch einen Roboter ohne die Einwirkung von sichtbarem
Licht, die daran anschließende automatisierte Detektion von motorischen Reaktionen der Fischeier auf optische Reize und
ein System zur automatisierten Verhaltensbeobachtung adulter Fische.
The zebrafish (Danio rerio) is a well-established vertebrate model organism. Its embryos are used extensively in biology and medicine to perform chemical screens to identify drug candidates or to ...evaluate teratogenicity and embryotoxicity of substances. Behavioral readouts are increasingly used to assess the effects of compounds on the nervous system. Early stage zebrafish show characteristic behavioral features at stages between 30 and 42 hours post fertilization (hpf) when exposed to a short and bright light flash. This so-called Photomotor Response (PMR) is a reaction of the nervous system of the fish and can be used as a marker in screenings for neuroactive chemicals. To probe a broad and diverse chemical space, many different substances have to be tested and repeated observations are necessary to warrant statistical significance of the results. Although PMR-based chemical screens must use a large number of specimens, there is no sophisticated, automated high-throughput platform available which ensures minimal human intervention. Here we report a PMR platform that was developed by combining an improved automatic sample handling with a remotely controllable microscope setup and an image analysis pipeline. Using infrared illumination during automatic sample preparation, we were able to eliminate excess amounts of visible light that could potentially alter the response results. A remotely controlled microscope setup allows us to screen entire 96-well microtiter plates without human presence that could disturb the embryos. The development of custom video analysis software, including single egg detection, enables us to detect variance among treated specimens and extract easy to interpret numerical values representing the PMR motion. By testing several neuroactive compounds we validated the workflow that can be used to analyze more than one thousand zebrafish eggs on a single 96-well plate.
As key-components of the urban-drainage system, storm-drains and manholes are essential to the hydrological modeling of urban basins. Accurately mapping of these objects can help to improve the ...storm-drain systems for the prevention and mitigation of urban floods. Novel Deep Learning (DL) methods have been proposed to aid the mapping of these urban features. The main aim of this paper is to evaluate the state-of-the-art object detection method RetinaNet to identify storm-drain and manhole in urban areas in street-level RGB images. The experimental assessment was performed using 297 mobile mapping images captured in 2019 in the streets in six regions in Campo Grande city, located in Mato Grosso do Sul state, Brazil. Two configurations of training, validation, and test images were considered. ResNet-50 and ResNet-101 were adopted in the experimental assessment as the two distinct feature extractor networks (i.e., backbones) for the RetinaNet method. The results were compared with the Faster R-CNN method. The results showed a higher detection accuracy when using RetinaNet with ResNet-50. In conclusion, the assessed DL method is adequate to detect storm-drain and manhole from mobile mapping RGB images, outperforming the Faster R-CNN method. The labeled dataset used in this study is available for future research.
This work proposes a new approach to the well-known method bat algorithm for solving the mobile robots global localization problem. The proposed method is leader-based bat algorithm (LBBA). The LBBA ...uses a small number of better micro-bats as leaders to influence the colony in the search for the best position, dealing satisfactorily with ambiguities during the localization process. The tests covered different scenarios aiming at comparing the proposed algorithm with other methods, such as the standard BA, the particle swarm optimization and particle filter. The results outperformed the compared methods, presenting a fast response and errors below the intended tolerance. The algorithm was tested in the robot kidnapping scenario and shows fast recovery in both simulation and in a real environment. In addition, the proposed technique showed 21% lower average error when compared with an algorithm that presents a variable quantity of particles, i.e. the adaptive Monte Carlo localization algorithm.
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