Data for: Above-ground dry mass and fruit geometries of 31 field muskmelon plants
Cite this dataset
He, Ke et al. (2024). Data for: Above-ground dry mass and fruit geometries of 31 field muskmelon plants [Dataset]. Dryad. https://doi.org/10.5061/dryad.mgqnk995f
Abstract
We collected a total of 751 fruits from 31 Cucumis melo L. var. agrestis Naud. plants, digitized the side profiles of these fruits, and applied an explicit re-expression of Preston’s equation (referred to as EPE hereinafter) to fit the planar coordinates of each fruit profile. By using the estimated parameters, we calculated the volume and surface area of each fruit. The black_white.zip file saves the black and white .bmp images at 600 dpi for the 751 fruits profiles. The edge_data.zip file includes the planar coordinates of each of the 751 fruits, and the EPE results.csv file includes the estimated parameters and goodness-of-fit of the EPE, and the fruit surface area and volume calculated by the surface area and volume formulas of the solid of revolution based on the EPE for each fruit. In addition, the EPE results.csv file also provides the measured volumes of the 751 fruits using the graduated cylinders. The MPG.csv file includes the total leaf dry mass, total stem dry mass, and total fruit volume of 31 C. melo var. Agrestis plants.
README: Profile data of Cucumis melo L. var. agrestis Naud. fruits
Description of the data and file structure
In the black_white.zip file, there are 751 .bmp images at 600 dpi. The image size was scaled to its actual size using the ratio of its actual fruit length measured to the fruit length in the scanned image. This means that the image size in a .bmp file is equal to the actual size of a fruit profile.
In the edge_data.zip file, there are 751 .csv files. In each .csv file, there are two columns, which record the x- and y-coordinates in cm for an arbitrary fruit's side profile.
In the EPE results.csv file, there are 18 columns.
(1) Image represents the fruit number. The number before the underline represents the individual plant number, and the number after the underline represents the fruit number of an individual plant.
(2) x0 represents the x-coordinate of the center of a fruit profile (in cm).
(3) y0 represents the y-coordinate of the center of a fruit profile (in cm).
(4) theta represents the angle between the midline of the fruit profile and the x-axis.
(5) a, b, c1, c2 and c3 are the estimated values of the parameters of the explicit Preston equation (see He et al. [2023] for details), where the units of a and b are cm, and c1, c2, and c3 are unitless.
(6) scan.length, scan.width and scan.area represent the scanned fruit length (in cm), maximum width (in cm) and planar area (in cm2), respectively.
(7) RSS represents the residual sum of squares in y-coordinates in cm2.
(8) sample.size represents the sample size, i.e., the number of data points on a fruit profile.
(9) RMSE represents the root-mean-square error in cm.
(10) V.pre and S.pre represent the predicted fruit volume (in cm3) and surface area (in cm2) using the volume and surface area formulas based on the explicit Preston equation with the estimated parameters, respectively.
(11) V.obs represents the volume (in cm3) measured using the graduated cylinder.
In the SE results.csv file, there are 20 columns.
(1) Image represents the fruit number. The number before the underline represents the individual plant number, and the number after the underline represents the fruit number of an individual plant.
(2) x0 represents the x-coordinate of the center of a fruit profile (in cm).
(3) y0 represents the y-coordinate of the center of a fruit profile (in cm).
(4) theta represents the angle between the midline of the fruit profile and the x-axis.
(5) a, k and n are the estimated values of the parameters of the superellipse equation (see Yao et al. [2024] for details), where the units of a and k are cm, and n are unitless.
(6) L, W and A represent the scanned fruit length (in cm), maximum width (in cm) and planar area (in cm2), respectively.
(8) RSS represents the residual sum of squares in y-coordinates in cm2.
(9) N represents the sample size, i.e., the number of data points on a fruit profile.
(10) RMS.IC represents the relative intrinsic curvature.
(10) RMS.PEC represents the root-mean-square relative parameter-effects curvature.
(10) Cri.C represents the critical curvature.
(11) n.Median, n.Mean and n.SD represent the median, mean, and standard deviation of parameter n, respectively.
(12) n.LCI and n.UCI represent the lower and upper bounds of the 95% confidence interval for parameter n, respectively.
In the GE results.csv file, there are 17 columns.
(1) Image represents the fruit number. The number before the underline represents the individual plant number, and the number after the underline represents the fruit number of an individual plant.
(2) x0 represents the x-coordinate of the center of a fruit profile (in cm).
(3) y0 represents the y-coordinate of the center of a fruit profile (in cm).
(4) theta represents the angle between the midline of the fruit profile and the x-axis.
(5) a, k, n1, n2 and n3 are the estimated values of the parameters of the Geilis equation (see Yao et al. [2024] for details), where the units of a and k are cm, and n1, n2 and n3 are unitless.
(6) RSS represents the residual sum of squares in y-coordinates in cm2.
(7) N represents the sample size, i.e., the number of data points on a fruit profile.
(8) L, W and A represent the scanned fruit length (in cm), maximum width (in cm) and planar area (in cm2), respectively.
(9) RMS.IC represents the relative intrinsic curvature.
(10) RMS.PEC represents the root-mean-square relative parameter-effects curvature.
(11) Cri.C represents the critical curvature.
In the MPG.csv file, there are 4 columns.
(1)Code represents the plant code of each of 31 C. melo var. agrestis plants.
(2)LeafM represents the total dry weight of all leaves for each plant.
(3)StemM represents the total dry weight of all stems for each plant.
(4)FruitV represents the total volume of all fruits for each plant.
Reference(s)
He, K.; Hui, C.; Yao, W.; Wang, J.; Wang, L.; Li, Q.; Shi, P. Evidence that field muskmelon (Cucumis melo L. var. agrestis Naud.) fruits are solids of revolution. Plants 2023, in press.
Yao, W.; Hui, C.; Wang, L.; Wang, J.; Gielis, J.; Shi, P. Comparison of the performance of two polar equations in describing the geometries of elliptical fruits. Bot. Lett. 2024, in press.
Methods
A total of 751 fruits from 31 Cucumis melo L. var. agrestis Naud. plants were collected for detailed study. Each fruit was photographed using a horizontal smartphone (iPhone 12, Zhengzhou, China), mounted on an adjustable tabletop phone mount, while placing the fruit on a test tube rack directly beneath the camera to ensure that the fruits were stably positioned horizontally and that the lens was focused on the fruit's center. To calibrate the deviation of the image size of each fruit from its actual size, we measured the maximum length of the fruit using a vernier caliper.
To obtain the planar coordinates of fruit 2D profiles, the photographs were converted into black-white images and saved as .bmp format using Adobe Photoshop CS2 (version 9.0; Adobe, San Jose, CA, USA). A program developed by Shi et al. (2018) and Su et al. (2019) developed in Matlab (version >= 2009a; MathWorks, Natick, MA, USA) was then used to extract the planar coordinates of each fruit profile from the corresponding .bmp black-white image.The function ‘fitEPE’ in the package ‘biogeom’ (version 1.3.5) (Shi et al., 2022) in R (version 4.2.1) (R Core Team, 2022) was used to estimate the numerical values of a, b, c1, c2, and c3. The Nelder-Mead optimization method was used to minimize the residual sum of squares (RSS) between the observed and predicted y-values of C. melo var. agrestis fruit profiles. After obtaining the estimated parameters of the EPE, we used the surface area and volume equations for the solid of revolution (Narushin et al., 2022) based on the EPE to calculate the fruit surface area and volume for each fruit of the 751 fruits.
To compare the predicted volume of a fruit with its observed volume, we measured volume by submerging each fruit in water in a 100 mL graduated cylinder with a diameter of 3 cm and reading the observed volume of displaced water. The results were saved in the EPE_results.csv file.
The above contents were cited from He et al. (2023).
References
- Narushin, V.G.; Romanov, M.N.; Griffin, D.K. Egg and math: Introducing a universal formula for egg shape. Ann. N. Y. Acad. Sci. 2021, 1505, 169–177.
- R Core Team. R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2022. Available online: https://www.r-project.org/ (accessed on 1 June 2022).
- Shi, P.; Gielis, J.; Niklas, K.J. Comparison of a universal (but complex) model for avian egg shape with a simpler model. Ann. N. Y. Acad. Sci. 2022, 1514, 34–42.
- Shi, P.; Ratkowsky, D.A.; Li, Y.; Zhang, L.; Lin, S.; Gielis, J. A general leaf area geometric formula exists for plants—Evidence from the simplified Gielis equation. Forests 2018, 9, 714.
- Su, J.; Niklas, K.J.; Huang, W.; Yu, X.; Yang, Y.; Shi, P. Lamina shape does not correlate with lamina surface area: An analysis based on the simplified Gielis equation. Glob. Ecol. Conserv. 2019, 19, e00666.
- He, K.; Hui, C.; Yao, W.; Wang, J.; Wang, L.; Li, Q.; Shi, P. Evidence that field muskmelon (Cucumis melo L. var. agrestis Naud.) fruits are solids of revolution. Plants 2023, in press.