Intrinsic Features of Blobs

Contents 1 Intrinsic Features for Blobs 1.1 Volume 1.2 Integrated Intensity 1.3 Centroid (unweighted and weighted) 1.4 Axes Lengths 1.5 Eccentricity 1.6 Elongation 1.7 Orientation 1.8 Bounding Box Volume 1.9 Oriented Bounding Box Volume 1.10 Sum 1.11 Mean 1.12 Median 1.13 Minimum 1.14 Maximum 1.15 Sigma 1.16 Variance 1.17 Radius Variation 1.18 Skew 1.19 Energy 1.20 Entropy 1.21 Surface Gradient 1.22 Interior Gradient 1.23 Interior Intensity 1.24 Surface Intensity 1.25 Intensity Ratio 1.26 Shared Boundary 1.27 Surface Area 1.28 Shape 2 Glossary of Notation 3 External Links

Intrinsic Features for Blobs

These features can be calculated with two input images (Data Image and Label Image). They are most commonly used for blob-like regions, such as cell nuclei.

Volume

Number of voxels in the object. (Dirk)

Integrated Intensity

Sum of the intensities of all voxels in the object. (Dirk)

Centroid (unweighted and weighted)

The unweighted centroid calculates the center of the object. The weighted centroid uses the image intensity values to calculate the intensity center of the object. (Dirk)

Axes Lengths

The length of the axes of the ND hyper-ellipsoid fit to the object. (Dirk)

Eccentricity

Ratio of the distance between the foci of the best-fit hyper-ellipsoid to the length of its major axis. (2D) (Dirk)

Elongation

Ratio of the major axis length to minor axis length of the best-fit hyper-ellipsoid. (2D) (Dirk)

Orientation

Angle between the major axis of the best-fit hyper-ellipsoid and origin. (2D) (Dirk)

Bounding Box Volume

Number of voxels in the bounding box of the object. (Dirk)

Oriented Bounding Box Volume

Number of voxels in the oriented bounding box of the object. The oriented bounding box is defined as the bounding box aligned along the axes of the object. (Dirk)

Sum

Same as integrated intensity (ITK statistics)

Mean

Average intensity of voxels in the object (ITK statistics)

Median

Middle intensity of voxels in the object (ITK statistics)

Minimum

Minimum intensity of voxels in the object (ITK statistics)

Maximum

Maximum intensity of voxels in the object (ITK statistics)

Sigma

Standard deviation of intensity of voxels in the object (ITK statistics)

Variance

Variance of intensity of voxels in the object (ITK statistics)

Radius Variation

Standard deviation of distance from surface voxels to centroid (Isaac)

Skew

Skew of the normalized intensity histogram (Isaac) (See Supplement B2)

Energy

Energy of the normalized intensity histogram (Isaac) (See Supplement B2)

Entropy

Entropy of the normalized intensity histogram (Isaac) (See Supplement B2)

Surface Gradient

Average of surface gradients (Isaac)

Interior Gradient

Average of interior gradients (Isaac)

Interior Intensity

Average of interior intensities (Isaac)

Surface Intensity

Average of surface intensities (Isaac)

Intensity Ratio

Ratio of surface intensity to interior intensity (Isaac)

Shared Boundary

Ratio of surface area that touches another object to total surface area (Isaac)

Surface Area

Number of voxels on surface of the object (Isaac)

Shape

Ratio of surface voxels to total voxels - compactness or thinness of object (Isaac) (See Supplement B2)

Glossary of Notation

p = (x,y,z) - the coordinate of a voxel (three-dimensional point in a volume image)
N_p - a neighbor voxel of p
l_p - the segmentation label at p
I_i(p) - the intensity value of p at i^th channel
Ω = {p | l_p = o} - the set of voxels of an object o
- the set of surface voxels of the object
Ω_in = Ω − Ω_s - the set of interior voxels of an object
G - the magnitude of intensity gradient at p
- the center of mass of the object
P - the normalized histogram of the intensities
P(I) - normalized histogram of intensity values I

External Links

itkLabelGeometryImageFilter

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