Evaluating geometric measurement accuracy based on 3D model reconstruction of nursery tomato plants by Agisoft photoscan software

Measuring the vegetation structure of a plant with the help of 3D images is a non-destructive method that can be used to monitor the plant’s status during the growing season. Structure from motion (SfM) is a popular optical distance measurement method that uses 2D images to create 3D models. Identifying factors that influence the precision of SfM is important due to its increasing use in phenotyping. The primary objectives of this study were, i) to scrutinize the impact of imaging parameters—including, color checkerboard location, overlap size of images, and background filtering—on the quality indices of 3D models, and ii) to attain precise measurements of leaf area, stem diameter, and height through the combination of images captured from different camera shooting angles. The three nursery tomato plants were photographed at every five-degree rotation of the turntable, five different locations of color checkerboards, and five camera shooting angles. Results indicated the color checkerboard’s presence and position affect the quality indices of the 3D models. Visually and by the lowest mean keypoint size value, the least noisy 3D model was obtained when the wall of the plant pot was covered with a checkerboard. When the base-to-distance (b/y) ratio as the image overlap index increased from 0.1 to 0.2, the generation time of the 3D models decreased by more than two times. Optimal Mean Absolute Percentage Error (MAPE) values of 1.08 %, 1.01 %, and 1.38 % were achieved for the estimation of leaf area, stem diameter, and height, respectively. This was recorded by using images taken at 0°, 30°, and 105° vertical azimuth angles. Constructing a 3D model by integrating images captured from other angles or more azimuth angles represents numerous visual challenges and leads to problems of point mismatch, which affects the accuracy of measurements.