PMC6783815_01
Processes of extracting the plant image from the micro-CT image. See Materials and Methods for details.
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Micro-CT images of plants were extracted from the captured images using ImageJ software ( Figures 1  and  3D, E ).
Cultured plant samples and its processing images. (A-C) Gemmalings (12 days old) of the wild-type line, Tak-1 (A), the Mpan knockout line Mpan-1ko
(B), and the complementation line, pMpAN:MpAN-1/Mpan-1ko
(C). Bars, 3 mm. (D, E) Transverse views of a pre-processed micro-computed tomography (micro-CT) image (D) and the extracted plant image via manual image processing as shown in 
Figure 1

(E). e plastic eraser, p plant, t plastic tube. (F-H) Reconstructed three-dimensional (3D) images of Tak-1 (F), Mpan-1ko
(G), and pMpAN:MpAN-1/Mpan-1ko
(H). (I, J) Convex hull image of reconstructed images of Tak-1 (I) and Mpan-1ko
(J). The convex hull image and extracted plant image are shown in magenta and green, respectively.
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Micro-CT images of plants were extracted from the captured images using ImageJ software ( Figures 1  and  3D, E ). These extracted images were reconstructed as 3D plant images ( Figures 3F-H ).
Morphological descriptors of 12-day-old gemmalings of Tak-1 (wild type (WT)), Mpan-1ko (Mutant), and pMpAN:MpAN-1/Mpan-1ko (Comp.) Relative object volume (A), relative convex volume (B), relative object surface area (C), relative convex surface area (D), convexity (E), and solidity (F) are shown in box-and-whisker plots. Median values (middle bars) and first to third interquartile ranges (boxes); whiskers indicate the interquartile ranges of ~1.5 A; dots indicate outliers. The data in (A-D) are indicated as relative value to mean of Tak-1. Circles indicate value of each individual. Asterisks indicate significant differences compared with Tak-1 (*P < 0.05, **P < 0.01, Student's t-test). N = 18. (G) Scatter plot of solidity versus convexity. Dashed black line is the classification boundary obtained by linear discriminant analysis using Tak-1 and Mpan-1ko.
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Based on the 3D convex hulls of the plant bodies, shown as magenta surfaces surrounding plant bodies in  Figure 3I  (Tak-1) and  3J  (Mpan-1ko), we measured volumes and areas of objects and convex hull ( Figures 4A-D ). Then, we used these values to calculate two 3D shape descriptors: convexity and solidity ( Figures 4E, F ). The values of these descriptors are shown as scatter plot of solidity versus convexity in  Figure 4G .