Using DeepLabCut for markerless cardiac physiology and toxicity estimation in water fleas (Daphnia magna)

Ferry Saputra; Michael Edbert Suryanto; Gilbert Audira; Cao Thang Luong; Chih-Hsin Hung; Marri Jmelou Roldan; Ross D Vasquez; Chung-Der Hsiao

doi:10.1016/j.aquatox.2023.106676

Using DeepLabCut for markerless cardiac physiology and toxicity estimation in water fleas (Daphnia magna)

Aquat Toxicol. 2023 Oct:263:106676. doi: 10.1016/j.aquatox.2023.106676. Epub 2023 Sep 4.

Authors

Ferry Saputra¹, Michael Edbert Suryanto¹, Gilbert Audira¹, Cao Thang Luong², Chih-Hsin Hung², Marri Jmelou Roldan³, Ross D Vasquez⁴, Chung-Der Hsiao⁵

Affiliations

¹ Department of Chemistry, Chung Yuan Christian University, Taoyuan 320314, Taiwan; Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan 320314, Taiwan.
² Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Da-Shu, Kaohsiung City 84001, Taiwan.
³ Department of Pharmacy, Faculty of Pharmacy, University of Santo Tomas, Manila 1015, Philippines; Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila 1015, Philippines.
⁴ Department of Pharmacy, Faculty of Pharmacy, University of Santo Tomas, Manila 1015, Philippines; Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila 1015, Philippines; The Graduate School, University of Santo Tomas, Manila 1015, Philippines.
⁵ Department of Chemistry, Chung Yuan Christian University, Taoyuan 320314, Taiwan; Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan 320314, Taiwan; Center for Nanotechnology, Chung Yuan Christian University, Taoyuan 320314, Taiwan; Research Center for Aquatic Toxicology and Pharmacology, Chung Yuan Christian University, Taoyuan 320314, Taiwan. Electronic address: cdhsiao@cycu.edu.tw.

PMID: 37689033
DOI: 10.1016/j.aquatox.2023.106676

Abstract

Daphnia magna is one species of water flea that has been used for a long time for ecotoxicity studies. In addition, Daphnia has a myogenic heart that is very useful for cardiotoxicity studies. Previous attempts to calculate the cardiac parameter endpoints in Daphnia suffer from the drawback of tedious operation and high variation due to manual counting errors. Even the previous method that utilized deep learning to help the process suffer from either overestimation of parameters or the need for specialized equipment to perform the analysis. In this study, we utilized DeepLabCut software previously used for animal pose tracking and demonstrated that ResNet_152 was the best fit for training the network. The trained network also showed comparable results with ImageJ and Kymograph, which was mostly done manually. In addition to that, several macro scripts in either Excel or Python format were developed to help summarize the data for faster analysis. The trained network was then challenged to analyze the potential cardiotoxicity of imidacloprid and pendimethalin in D. magna, and it showed that both pesticides cause alteration in their cardiac performance. Overall, this method provides a simple and automatic method to analyze the cardiac performance of Daphnia by utilizing DeepLabCut. The method proposed in this paper can contribute greatly to scientists conducting fast and accurate cardiotoxicity measurements when using Daphnia as a model.

Keywords: Cardiac physiology; Cardiotoxicity; Daphnia; DeepLabCut; Water flea.