color.plot
(Package: GiNA) :
Analyzing the digital color of objects
This function was design to assess the color output of the scanCRAN function by drawing the digital color detected by the program in a way that the user can assess the colors that the computer is detecting for each object in the picture.
GiNA-package
(Package: GiNA) :
Software for high throughput phenotyping of fruit crops
GiNA is a package designed for automatic highthoroughput phenotyping analysis of images. The program was conceived to read files with .JPG and .TIFF extensions (which stands for Joint Picture Experts Group) and uses image segmentation based on the EBImage package in order to recognize fruits and compute its features such as area, perimeter, color (in 3 channels), shape and volume to be used for GWAS, QTL or descriptive studies. The core of the package relays in 3 functions; 1) cutoff is the function in charge of determining the best cut off value for segmentation, the color scale in R goes from 0 to 1 and in other siftwares from 0 to 265, the function detects the color of the background (black or white) and returns several pictures of segmentation at different cutoff values in order to pick the most suitable for your crop, 2) pixArea reads the pictures and returns a plot with the pixel area for each object in the picture in order to provide an estimate of the minimum value to use in the real analysis, the value obtained from this function should be passed to the scanCRAN function as the minArea to discard all noise from the picture, 3) scanCRAN is the core of the package and performs image analysis for all pictures stored in the folder path provided at the cutoff value selected. The output from the scanCRAN function is a list structure with each element of the list being a dataframe with all measurements for the fruits or objects found in the picture.
scanCRAN
(Package: GiNA) :
High throughput phenotyping using scanCRAN
This function is the core of the GiNA package which is in charge of reading the pictures find in the folder provided and perform the image segmentation in order to find the objects in the picture (i.e. fruits) and measure parameters such as area, perimeter, shape, volume, gray color, red, green and blue color.
jet.scan
(Package: GiNA) :
Assessing variability for measurements using jet plot
Same than color.plot function, this function was designed to assess the results from the scanCRAN function by providing the output of such function and draw plots showing the variation found in the objects measured in each object.
Even not required, the average value area in pixels for the objects analyzed is a parameter of interest when the objects to be analyzed are particularly small such as seeds or extremely small fruits. Therefore, the use of this function provides a plot of the are in pixels for all the objects in the picture for a given cutoff value provided. Once the value has determined this can be provided to the scanCRAN function in the argument 'minArea' to make the function perform faster.
cutoff
(Package: GiNA) :
Finding the optimal cutoff value for segmentation
This function reads the picture provided in a path and performs image segmentation in a gray scale version of the picture at different values of color between 0 and 1 depending of the background color. If the background is black the function will segment the picture at values of 0.01 to 0.12 and if a white background is used values 0.5 to 0.8 will be used in order to determine the optimal value of segmentation, such values can be modified by the user in the argument 'prefs'. The resulting images at different cutoff values will be stored in a folder created with the name 'cutoff_vals' in the same folder provided by the user.