PlanCoor: Extracts the Planar Coordinates the 2-D Profiles of Apical...

In biogeom: Biological Geometries

Extracts the Planar Coordinates the 2-D Profiles of Apical Meristems

Description

PlanCoor is used to extract the planar coordinates the 2-D profiles of shoot or root apical meristems in grayscale bitmap (.bmp) images saved in a folder.

Usage

PlanCoor( folder.name, lower.val = 0, upper.val = 250, ratio = 1,  
          fig.opt = TRUE, np = NULL, unit = "unitless", verbose = TRUE )

Arguments

folder.name	the name of a folder that saves the 2-D profiles of shoot or root apical meristems in grayscale .bmp images
lower.val	the lower bound of pixel values for selecting an AM's profile curve from a grayscale image.
upper.val	the upper bound of pixel values for selecting an AM's profile curve from a grayscale image.
ratio	the scaling factor between the actual image dimensions and the desired coordinate system scale.
fig.opt	an optional argument to draw the extracted the AM's profile curve.
np	the number of data points forming an AM's profile curve.
unit	the unit of the x-axis and the y-axis when showing an AM's profile curve.
verbose	an optional argument allowing the user to suppress the printing of computation progress.

Details

The apical meristem profiles are recommended to be extracted using the Pen Tool in Adobe Photoshop (version >= 22.4.2; Adobe, San Jose, CA, USA) and saved as grayscale bitmap (.bmp) images. In each image, the profile should be depicted in black or a gray value close to black, whereas the remaining areas should be set to white (with pixel values of 255). All profiles are recommended to be adjusted to form downward-opening curves using Adobe Photoshop. The resulting profiles are to be saved in a folder within the current R working directory. The name of this folder is used as an argument folder.name in the PlanCoor function. Users can adjust the values of lower.val and upper.val to enhance the clarity of the shoot or root apical meristem profiles. The argument ratio represents the scaling factor between the actual image dimensions and the desired coordinate system scale. For example, if an image has a width of 7 cm and a height of 10 cm, setting ratio = 2 will result in x- and y-coordinates being mapped to a window of 14 cm by 20 cm. The default of np is NULL, and the number of data points forming an AM's profile curve depends on the resolution of the image and the size of the extracted AM's profile. If the use defines an integer such as 500, the final number of data points is equal to the minimum value of 500 and the number of data point when np = NULL.

Value

FileName	the names of the files in the folder but removing the file extension (e.g., "myimage" from a file named "myimage.bmp" by dropping its extension ".bmp").
x	the x-coordinates of the profile curve(s).
y	the y-coordinates of the profile curve(s).

Note

In the folder, one image is also allowed. Assume that all grayscale .bmp images are saved in a folder named "Image" in the current working directory. Using PlanCoor(folder.name = "Image", fig.opt = FALSE) can obtain the x- and y-coordinates of the profiles.

\quad The PlanCoor function can also be used to extract two-dimensional profiles of other objects, such as leaves. The leaf profile can first be obtained using image processing software (e.g., Adobe Photoshop). It is recommended to fill the exterior of the leaf profile in black and the interior in white. In such cases, the values of lower.val and upper.val should be adjusted accordingly to ensure a clear leaf profile is extracted.

Author(s)

Peijian Shi [e-mail], Johan Gielis [e-mail], Brady K. Quinn [e-mail].

References

Shi, P., Chen, L., Quinn, B.K., Yu, K., Miao, Q., Guo, X., Lian, M., Gielis, J., Niklas, K.J. (2023) A simple way to calculate the volume and surface area of avian eggs. Annals of the New York Academy of Sciences 1524, 118-131. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/nyas.15000")}

See Also

fitAM, SAMs, SurfaceAreaAM, VolumeAM

Examples

  folder_path1 <- system.file("extdata", "SAM", package="biogeom")
  bmp.res1     <- PlanCoor( folder_path1, lower.val = 0, upper.val = 250, 
                            fig.opt = TRUE, np = NULL )

  folder_path2 <- system.file("extdata", "Leaf", package="biogeom")
  bmp.res2     <- PlanCoor( folder_path2, lower.val = 1, upper.val = 254, 
                            fig.opt = TRUE, np = NULL, unit = "cm", verbose = FALSE )

  graphics.off()

biogeom documentation built on Aug. 24, 2025, 5:08 p.m.