In this tutorial video, Kevin from Department of Chemistry, Chung Yuan Christian University will introduce how to use StarDist method to do image segmentation and duckweed counting in an automatic manner. In recent years, there have been efforts to utilize surface water as a power source, materials, and food. However, these efforts are impeded due to the vast amounts of contaminants and emerging contaminants introduced by anthropogenic activities. Herbicides such as Roundup and Glufosinate are commonly known to contaminate surface water through agricultural industries. in contrast, some emerging contaminants, such as rare earth elements, have started to enter the surface water from the production and waste of electronic products. Duckweeds are angiosperms from the Lemnaceae family and have been used for toxicity tests in aquatic environments, mainly those from the genus Lemna, and have been approved by OECD. In this study, we used duckweed from the genus Wolffia, which is smaller and considered a good indicator of metal pollutants in the aquatic environment. The growth rate of duckweed is the most common endpoint in observing pollutant toxicity. In order to observe and mark the fronds automatically, we used StarDist, a machine learning-based tool. StarDist is available as a plugin in ImageJ, simplifying and assisting the counting process. Python also helps arrange, manage, and calculate the inhibition percentage after duckweeds are exposed to contaminants. In summary, we can provide a workflow for automatic frond counting using StarDist integrated with ImageJ and Python to simplify the detection, counting, data management, and calculation process.
www.mdpi.com/2...
Kurnia, K.A.; Lin, Y.-T.; Farhan, A.; Malhotra, N.; Luong, C.T.; Hung, C.-H.; Roldan, M.J.M.; Tsao, C.-C.; Cheng, T.-S.; Hsiao, C.-D. Deep Learning-Based Automatic Duckweed Counting Using StarDist and Its Application on Measuring Growth Inhibition Potential of Rare Earth Elements as Contaminants of Emerging Concerns. Toxics 2023, 11, 680. doi.org/10.339...