public class SpotMorphologyAnalyzer<T extends RealType<T>> extends IndependentSpotFeatureAnalyzer<T>
SpotAnalyzercomputes morphology features for the given spots.
It estimates shape parameters by computing the most resembling ellipsoid from the pixels contained within the spot radius. From this ellipsoid, it determines what are its semi-axes lengths, and their orientation.
In the 3D case, the features ELLIPSOIDFIT_SEMIAXISLENGTH_* contains the semi-axes lengths, ordered from the largest (A) to the smallest (C). ELLIPSOIDFIT_AXISPHI_* and ELLIPSOIDFIT_AXISTHETA_* give the orientation angles of the corresponding ellipsoid axis, in spherical coordinates. Angles are expressed in radians.
In the 2D case, ELLIPSOIDFIT_SEMIAXISLENGTH_A and ELLIPSOIDFIT_AXISPHI_A are always 0, the THETA angles are 0, and ELLIPSOIDFIT_AXISPHI_B and ELLIPSOIDFIT_AXISPHI_C differ by π/2.
From the semi-axis length, a morphology index is computed. Spots are
classified according to the shape of their most-resembling ellipsoid. We look
for equality between semi-axes, with a certain tolerance, which value is
In the 2D case, if b > c are the semi-axes length
In the 2D case, if a > b > c are the semi-axes length
SpotMorphologyAnalyzerFactory.OBLATE: the spot resembles a flat disk
SpotMorphologyAnalyzerFactory.PROLATE: the spot resembles a rugby ball
SpotMorphologyAnalyzerFactory.SCALENE; the spot's shape has nothing particular
|Modifier and Type||Field and Description|
Significance factor to determine when a semiaxis length should be considered significantly larger than the others.
|Constructor and Description|
|Modifier and Type||Method and Description|
checkInput, getErrorMessage, getProcessingTime, process
public static final double SIGNIFICANCE_FACTOR
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