Dataset Information

Zebrafish behavior feature recognition using three-dimensional tracking and machine learning.

ABSTRACT: In this work, we aim to construct a new behavior analysis method by using machine learning. We used two cameras to capture three-dimensional (3D) tracking data of zebrafish, which were analyzed using fuzzy adaptive resonance theory (FuzzyART), a type of machine learning algorithm, to identify specific behavioral features. The method was tested based on an experiment in which electric shocks were delivered to zebrafish and zebrafish swimming was tracked in 3D simultaneously to find electric shock-associated behaviors. By processing the obtained data with FuzzyART, we discovered that distinguishing behaviors were statistically linked to the electric shock based on the machine learning algorithm. Moreover, our system could accept user-supplied data for detection and quantitative analysis of the behavior features, such as the behavior features defined by the 3D tracking analysis above. This system could be applied to discover new distinct behavior features in mutant zebrafish and used for drug administration screening and cognitive ability tests of zebrafish in the future.

SUBMITTER: Yang P

PROVIDER: S-EPMC8242018 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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Zebrafish behavior feature recognition using three-dimensional tracking and machine learning.

Yang Peng P Takahashi Hiro H Murase Masataka M Itoh Motoyuki M

Scientific reports 20210629 1

In this work, we aim to construct a new behavior analysis method by using machine learning. We used two cameras to capture three-dimensional (3D) tracking data of zebrafish, which were analyzed using fuzzy adaptive resonance theory (FuzzyART), a type of machine learning algorithm, to identify specific behavioral features. The method was tested based on an experiment in which electric shocks were delivered to zebrafish and zebrafish swimming was tracked in 3D simultaneously to find electric shock ...[more]

PMID: 34188116

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Project description:BackgroundHigh-throughput behavioral analysis is important for drug discovery, toxicological studies, and the modeling of neurological disorders such as autism and epilepsy. Zebrafish embryos and larvae are ideal for such applications because they are spawned in large clutches, develop rapidly, feature a relatively simple nervous system, and have orthologs to many human disease genes. However, existing software for video-based behavioral analysis can be incompatible with recordings that contain dynamic backgrounds or foreign objects, lack support for multiwell formats, require expensive hardware, and/or demand considerable programming expertise. Here, we introduce Marigold, a free and open source web app for high-throughput behavioral analysis of embryonic and larval zebrafish.ResultsMarigold features an intuitive graphical user interface, tracks up to 10 user-defined keypoints, supports both single- and multiwell formats, and exports a range of kinematic parameters in addition to publication-quality data visualizations. By leveraging a highly efficient, custom-designed neural network architecture, Marigold achieves reasonable training and inference speeds even on modestly powered computers lacking a discrete graphics processing unit. Notably, as a web app, Marigold does not require any installation and runs within popular web browsers on ChromeOS, Linux, macOS, and Windows. To demonstrate Marigold's utility, we used two sets of biological experiments. First, we examined novel aspects of the touch-evoked escape response in techno trousers (tnt) mutant embryos, which contain a previously described loss-of-function mutation in the gene encoding Eaat2b, a glial glutamate transporter. We identified differences and interactions between touch location (head vs. tail) and genotype. Second, we investigated the effects of feeding on larval visuomotor behavior at 5 and 7 days post-fertilization (dpf). We found differences in the number and vigor of swimming bouts between fed and unfed fish at both time points, as well as interactions between developmental stage and feeding regimen.ConclusionsIn both biological experiments presented here, the use of Marigold facilitated novel behavioral findings. Marigold's ease of use, robust pose tracking, amenability to diverse experimental paradigms, and flexibility regarding hardware requirements make it a powerful tool for analyzing zebrafish behavior, especially in low-resource settings such as course-based undergraduate research experiences. Marigold is available at: https://downeslab.github.io/marigold/ .

Project description:Poultry behavior indicates their health, welfare, and production performance. Timely access to broilers' behavioral information can improve their welfare and reduce disease spread. Most behaviors require a period of observation before they can be accurately judged. However, the existing approaches for multi-object behavior recognition were mostly developed based on a single-frame image and ignored the temporal features in videos, which led to misrecognition. This study proposed an end-to-end method for recognizing multiple simultaneous behavioral events of cage-free broilers in videos by Broiler Behavior Recognition System (BBRS) based on spatiotemporal feature learning. The BBRS consisted of 3 main components: the improved YOLOv8s detector, the Bytetrack tracker, and the 3D-ResNet50-TSAM model. The basic network YOLOv8s was improved with MPDIoU to identify multiple broilers in the same frame of videos. The Bytetrack tracker was used to track each identified broiler and acquire its image sequence of 32 continuous frames as input for the 3D-ResNet50-TSAM model. To accurately recognize behavior of each tracked broiler, the 3D-ResNet50-TSAM model integrated a temporal-spatial attention module for learning the spatiotemporal features from its image sequence and enhancing inference ability in the case of its image sequence less than 32 continuous frames due to its tracker ID switching. Each component of BBRS was trained and tested with the rearing density of 7 to 8 birds/m2. The results demonstrated that the mAP@0.5 of the improved YOLOv8s detector was 99.50%. The Bytetrack tracker achieved a mean MOTA of 93.89% at different levels of occlusion. The Accuracy, Precision, Recall, and F1score of the 3D-ResNet50-TSAM model were 97.84, 97.72, 97.65, and 97.68%, respectively. The BBRS showed satisfactory inference ability with an Accuracy of 93.98% when 26 continuous frames of the tracked broiler were received by the 3D-ResNet50-TSAM model. This study provides an efficient tool for automatically and accurately recognizing behaviors of cage-free multi-broilers in videos. The code will be released on GitHub (https://github.com/CoderYLH/BBRS) as soon as the study is published.

Dataset Information

Zebrafish behavior feature recognition using three-dimensional tracking and machine learning.

Publications

Zebrafish behavior feature recognition using three-dimensional tracking and machine learning.

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