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
Abstract
:1. Introduction
2. Material and Methods
2.1. Duckweed Culture
2.2. Preparation of Stock Solution
2.3. Toxicity Test and Image Acquisition
2.4. Image Training by StarDist
2.5. Duckweed Detection and Counting
2.6. Mass Data Processing Using Python-Based Scripts
2.7. Statistical Tests
3. Results
3.1. Overview of Experimental Workflow
3.2. Segmentation Performance for Common Watermeal (Wolffia globosa)
3.3. Determining the Optimal Overlap/Non-Maximum Suppression (NMS) Threshold for Wolffia globosa Detection Using StarDist 2D
3.4. Optimized StarDist Model for Duckweed Growth Inhibition Assay
3.5. Exposure to Rare Earth Elements Alters Wolffia globosa Growth Rate
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Plant Species | Endpoints | Manual/Auto | Software and References |
---|---|---|---|
Wolffia globosa | Duckweed fronds counting based on the size and shape of objects | Automatic | QuPath (pre-training) and StarDist (Training and processing) (This study) |
Wolffia globosa | EC50 determination through biomass weight | Manual | None [29] |
Lemna gibba | Duckweed frond counting based on image recording and frond area interpretation based on color intensity | Automatic | Nikon ACT-2U (Area measurement) and Assess: Image Analysis Software for Plant Disease Quantification (Frond area interpretation) [24] |
Lemna minor | Differentiation between live and dead duckweed | Automatic | NI Vision Assistant [27] |
Landoltia punctata | Manual counting using a magnifying glass | Manual | None [30] |
Lemna minor | Differentiation between live and dead duckweed and counting | Automatic | ACD-See (pre-processing) and Image Pro-Plus (processing) [31] |
Lemna minor | Duckweed fronds counting | Manual | None [32] |
Compound | Atomic Number | Valence Electron | Group | Day 7 IC50 (ppm) | Ln Milliken Charge | Aromatic Cavg Charge |
---|---|---|---|---|---|---|
Glyphosate | - | - | Herbicide | 36.4 | - | - |
Glufosinate | - | - | Herbicide | 34.0 | - | - |
Lanthanum | 57 | 5d16s2 | LREE | 31.9 | 1.900 | −0.432 |
Cerium | 58 | 4f15d16s2 | LREE | 21.3 | 1.905 | −0.434 |
Praseodymium | 59 | 4f36s2 | LREE | 117.8 | 1.980 | −0.441 |
Neodymium | 60 | 4f46s2 | LREE | 82.7 | 1.938 | −0.439 |
Samarium | 62 | 4f66s2 | LREE | 279.4 | 1.946 | −0.443 |
Europium | 63 | 4f76s2 | LREE | 158.2 | 1.877 | −0.443 |
Gadolinium | 64 | 4f75d16s2 | LREE | 122.4 | 2.158 | −0.455 |
Terbium | 65 | 4f96s2 | HREE | 260.3 | 2.190 | −0.45 |
Dysprosium | 66 | 4f106s2 | HREE | 14.6 | 2.138 | −0.454 |
Holmium | 67 | 4f116s2 | HREE | 16.5 | 2.168 | −0.458 |
Erbium | 68 | 4f126s2 | HREE | 15.5 | 2.175 | −0.461 |
Thulium | 69 | 4f136s2 | HREE | 146.3 | 2.117 | −0.461 |
Ytterbium | 70 | 4f146s2 | HREE | 195.8 | 2.004 | −0.455 |
Lutetium | 71 | 4f145d16s2 | HREE | 187.9 | 2.254 | −0.460 |
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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. https://doi.org/10.3390/toxics11080680
Kurnia KA, Lin Y-T, Farhan A, Malhotra N, Luong CT, Hung C-H, Roldan MJM, 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(8):680. https://doi.org/10.3390/toxics11080680
Chicago/Turabian StyleKurnia, Kevin Adi, Ying-Ting Lin, Ali Farhan, Nemi Malhotra, Cao Thang Luong, Chih-Hsin Hung, Marri Jmelou M. Roldan, Che-Chia Tsao, Tai-Sheng Cheng, and Chung-Der Hsiao. 2023. "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 11, no. 8: 680. https://doi.org/10.3390/toxics11080680