Table 1 

Quantitative phenotype descriptors and their descriptions 

Descriptor name 
Formula 
Description 


Size 



Area 
See description 
The total number of pixels identified during segmentation. 
Change in area 
Area(t)  Area(t1) 
The area of the parasite in the current frame at time t minus the area of the parasite in the previous frame (time t1). 


Shape 



End point length/Skeleton length 
See description 
Ratio of the Euclidean length of the shortest line between the two endpoints of the skeleton to the length of the skeleton. The skeleton is created by thinning the segmented region until it is represented by a line corresponding to the curve of the body. Branching of the skeleton is handled by iteratively applying the MATLAB spur operator that identifies and removes isolated edge points until only two edges remain [47]. 


Movement 



Image difference 
Image(t1)  Image(t) 
The number of pixels that moved from time t1 to t of the parasite. 
Perimeter (also for description of size) 
See description 
The number of pixels representing the boundary of the segmented region. 
Axis ratio (also for shape description) 
MinorAxisLength/MajorAxisLength 
Ratio of the minor axis length to the major axis length. The major and minor axes are computed for an ellipse with the same normalized second central moments as the region. 


Texture 



Entropy 
sum(p.*log_{2}p) 
Statistical measure of randomness related to the texture of an image where p contains the grayscale histogram. 
Contrast 
Σij^{2}p(i,j) 
The intensity contrast between a pixel and its neighbors throughout the region. 
Correlation 
The intensity correlation between a pixel and its neighbors. 

Energy 
The sum of the squared elements in the GLCM (graylevel cooccurrence matrix). The GLCM measures how often two intensities occur side by side. 

Homogeneity 
Measures the closeness of the distribution of the elements in the GLCM to the GLCM diagonal. 



Color 



Average grayscale 
See description 
The mean intensity value and standard deviation found in the region. 
Average red 

Average green 

Average blue 



Grayscale histogram 
See description 
A histogram with bins 0255 representing the count of each intensity value present in the region. 
Red histogram 

Green histogram 

Blue histogram 



Lee et al. BMC Genomics 2012 13(Suppl 1):S4 doi:10.1186/1471216413S1S4 