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(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

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The intensity correlation between a pixel and its neighbors.

Energy

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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

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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


Lee et al. BMC Genomics 2012 13(Suppl 1):S4   doi:10.1186/1471-2164-13-S1-S4

Open Data