Development of an Image Analysis Pipeline to Estimate Sphagnum Colony Density in the Field
Abstract
:1. Introduction
2. Materials and Methods
2.1. Site Selction
2.2. Field Image Acquisition
2.3. Image Processing Pipeline
2.4. Thresholding Channel Selection
2.5. Pipeline Validation
2.6. Statistical Analysis
3. Results
3.1. Development of an Image Processing and Analysis Pipeline
3.1.1. Pre-Processing Pipeline
3.1.2. Thresholding Optimisation
3.1.3. Thresholding and Annotation Channel Selection
3.1.4. Blob Detection and Capitula Counting
3.2. Estimation of Pipeline Accuracy
3.3. Estimation of Capitula Density in Field Images
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Location | Species | Subgenus | n. of Images |
---|---|---|---|
Coed y Darren | S. quinquefarium Warnstorf 1886 | Acutifolia | 23 |
Pen y Garn | S. fallax Klinggräff 1881 | Cuspidata | 9 |
S. inundatum Russow 1894 | Subsecunda | 4 | |
S. papillosum Lindberg 1872 | Sphagnum | 12 | |
S. fallax & S. papillosum (mix) | 5 | ||
Llyn Pendam | S. auriculatum Schimp. | Subsecunda | 11 |
S. fallax | Cuspidata | 10 | |
S. papillosum | Sphagnum | 8 | |
Total | 82 |
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van de Koot, W.Q.M.; van Vliet, L.J.J.; Chen, W.; Doonan, J.H.; Nibau, C. Development of an Image Analysis Pipeline to Estimate Sphagnum Colony Density in the Field. Plants 2021, 10, 840. https://doi.org/10.3390/plants10050840
van de Koot WQM, van Vliet LJJ, Chen W, Doonan JH, Nibau C. Development of an Image Analysis Pipeline to Estimate Sphagnum Colony Density in the Field. Plants. 2021; 10(5):840. https://doi.org/10.3390/plants10050840
Chicago/Turabian Stylevan de Koot, Willem Q. M., Larissa J. J. van Vliet, Weilun Chen, John H. Doonan, and Candida Nibau. 2021. "Development of an Image Analysis Pipeline to Estimate Sphagnum Colony Density in the Field" Plants 10, no. 5: 840. https://doi.org/10.3390/plants10050840