Mycelial growth assessment by digital image analysis in R software environment
This study was aimed at developing a script in R to assess fungal growth in Petri dishes using computer vision. The script was developed to aid studies in agricultural phytopathology. The fungi used were Elsinoe ampelina, Fusarium oxysporum and Fusarium verticillioides. The images were analyzed with...
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| Autores principales: | , , |
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| Lenguaje: | English |
| Publicado: |
Universidad de Tarapacá. Facultad de Ciencias Agronómicas
2017
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| Materias: | |
| Acceso en línea: | http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0718-34292017000100002 |
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| Sumario: | This study was aimed at developing a script in R to assess fungal growth in Petri dishes using computer vision. The script was developed to aid studies in agricultural phytopathology. The fungi used were Elsinoe ampelina, Fusarium oxysporum and Fusarium verticillioides. The images were analyzed with R and the EBImage package. The command computeFeatures.shape was used to calculate the area and the mean diameter of the colony and the label in square pixels. The script was run in a loop to automate the analysis of all images in sequence. The script developed in R with the package EBImage was able to recognize and measure the fungus colonies examined. Simultaneously with photographing, the mean diameter of colonies was obtained by calculating the arithmetic mean of the diameter measured with two straight perpendicular lines using a ruler. Using the mean diameter, the area of the colony was calculated as a circle. The coefficient of determination and the root mean square error were calculated using the measurements and the values obtained with the program. Based on the coefficient of determination, the measurements obtained with the software are similar to those made using a ruler. The script reduces the image analysis time and increases accuracy, especially for non-uniform colonies. |
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