Quantification and clustering of phenotypic screening data using time-series analysis for chemotherapy of schistosomiasis

Lee, Hyokyeong; Moody-Davis, Asher; Saha, Utsab; Suzuki, Brian M; Asarnow, Daniel; Chen, Steven; Arkin, Michelle; Caffrey, Conor R; Singh, Rahul

doi:10.1186/1471-2164-13-S1-S4

Table 1 Quantitative phenotype descriptors and their descriptions

From: Quantification and clustering of phenotypic screening data using time-series analysis for chemotherapy of schistosomiasis

Descriptor name	Formula	Description
Size
Area	See description	The total number of pixels identified during segmentation.
Change in area	Area(t) - Area(t-1)	The area of the parasite in the current frame at time t minus the area of the parasite in the previous frame (time t-1).
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(t-1) - Image(t)	The number of pixels that moved from time t-1 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.*log₂p)	Statistical measure of randomness related to the texture of an image where p contains the grayscale histogram.
Contrast	Σ\|i-j\|²p(i,j)	The intensity contrast between a pixel and its neighbors throughout the region.
Correlation	$\sum_{i, j} \frac{(i - μ i) (j - μ j) p (i, j)}{σ_{i} σ_{j}}$	The intensity correlation between a pixel and its neighbors.
Energy	$\sum_{i, j} {p (i, j)}^{2}$	The sum of the squared elements in the GLCM (gray-level co-occurrence matrix). The GLCM measures how often two intensities occur side by side.
Homogeneity	$\sum_{i, j} \frac{p (i, j)}{1 + \| i - j \|}$	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 0-255 representing the count of each intensity value present in the region.
Red histogram
Green histogram
Blue histogram

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ISSN: 1471-2164

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