Nyxus provided features
Pixel intensity features:
Nyxus feature code |
Description |
|---|---|
INTEGRATED_INTENSITY |
Integrated intensity of the region of interest (ROI) |
MEAN |
Mean intensity value of the ROI |
MEDIAN |
The median value of pixels in the ROI |
MIN |
Minimum intensity value in the ROI |
MAX |
Maximum intensity value in the ROI |
RANGE |
Range between the maximmu and minimum |
STANDARD_DEVIATION |
Standard deviation |
STANDARD_ERROR |
Standard error |
SKEWNESS |
Skewness - the 3rd standardized moment |
KURTOSIS |
Kurtosis - the 4th standardized moment |
HYPERSKEWNESS |
Hyperskewness - the 5th standardized moment |
HYPERFLATNESS |
Hyperflatness - the 6th standardized moment |
MEAN_ABSOLUTE_DEVIATION |
Mean absolute devation |
ENERGY |
ROI energy |
ROOT_MEAN_SQUARED |
Root of mean squared deviation |
ENTROPY |
ROI entropy - a measure of the amount of information (that is, randomness) in the ROI |
MODE |
The mode value of pixels in the ROI - the value that appears most often in a set of ROI intensity values |
UNIFORMITY |
Uniformity - measures how uniform the distribution of ROI intensities is |
UNIFORMITY_PIU |
Percent image uniformity, another measure of intensity distribution uniformity |
P01, P10, P25, P75, P90, P99 |
1%, 10%, 25%, 75%, 90%, and 99% percentiles of intensity distribution |
INTERQUARTILE_RANGE |
Distribution’s interquartile range |
ROBUST_MEAN_ABSOLUTE_DEVIATION |
Robust mean absolute deviation |
MASS_DISPLACEMENT |
ROI mass displacement |
Morphology features:
Nyxus feature code |
Description |
|---|---|
AREA_PIXELS_COUNT |
ROI area in the number of pixels |
AREA_UM2 |
ROI area in metric units |
CENTROID_X |
X-coordinate of the enter point of the ROI |
CENTROID_Y |
Y-coordinate of the center point of the ROI |
COMPACTNESS |
Mean squared distance of the object’s pixels from the centroid divided by the area. Compactness of a filled circle is 1, compactness of irregular objects or objects with holes is greater than 1 |
BBOX_YMIN |
Y-position and size of the smallest axis-aligned box containing the ROI |
BBOX_XMIN |
X-position and size of the smallest axis-aligned box containing the ROI |
BBOX_HEIGHT |
Height of the smallest axis-aligned box containing the ROI |
BBOX_WIDTH |
Width of the smallest axis-aligned box containing the ROI |
MAJOR_AXIS_LENGTH |
Length (in pixels) of the major axis of the ellipse that has the same normalized second central moments as the region |
MINOR_AXIS_LENGTH |
Length (in pixels) of the minor axis of the ellipse that has the same normalized second central moments as the region |
ECCENTRICITY |
Ratio of ROI’s inertia ellipse focal distance over the major axis length |
ORIENTATION |
Angle between the 0th axis and the major axis of the ellipse that has same second moments as the region |
ROUNDNESS |
Represents how similar a ROI’s inertia ellipse is to circle. Calculated based on the major and minor exis lengths |
EXTENT |
Proportion of the pixels (2D) or voxels (3D) in the bounding box that are also in the region. Computed as the area/volume of the object divided by the area/volume of the bounding box |
ASPECT_RATIO |
The ratio of the major axis to the minor axis of ROI’s inertia ellipse |
CONVEX_HULL_AREA |
Area of ROI’s convex hull |
SOLIDITY |
Ratio of pixels in the ROI common with its convex hull image |
PERIMETER |
Number of pixels in ROI’s contour |
EQUIVALENT_DIAMETER |
Diameter of a circle with the same area as the ROI |
EDGE_MEAN_INTENSITY |
Mean intensity of ROI’s contour pixels |
EDGE_STDDEV_INTENSITY |
Standard deviation of ROI’s contour pixels |
EDGE_MAX_INTENSITY |
Maximum intensity of ROI’s contour pixels |
EDGE_MIN_INTENSITY |
Minimum intensity of ROI’s contour pixels |
CIRCULARITY |
Represents how similar a shape is to circle. Clculated based on ROI’s area and its convex perimeter |
EROSIONS_2_VANISH |
Number of erosion operations for a ROI to vanish in its axis aligned bounding box |
EROSIONS_2_VANISH_COMPLEMENT |
Number of erosion operations for a ROI to vanish in its convex hull |
FRACT_DIM_BOXCOUNT |
Fractal dimension determined by the box counting method according to ISO 9276-6. If C is a fractal set, with fractal dimension DF < D, then the number N of boxes of size R needed to cover the set scales as R^(-DF). DF is known as the Hausdorf dimension, or Kolmogorov capacity, or Kolmogorov dimension, or simply box-counting dimension |
FRACT_DIM_PERIMETER |
Fractal dimension determined by the perimeter method according to ISO 9276-6. If we approximate ROI’s contour with rulers of length lambda, the perimeter based fractal dimension is the slope of the best fit line of log ROI perimeter versus log lambda, subtracted from 1 |
WEIGHTED_CENTROID_Y |
X-coordinate of centroid |
WEIGHTED_CENTROID_X |
Y-coordinate of centroid |
MIN_FERET_DIAMETER |
Feret diameter (or maximum caliber diameter) is the longest distance between any two ROI points along the same (horizontal) direction. This feature is the minimum Feret diameter for angles ranging 0 to 180 degrees |
MAX_FERET_DIAMETER |
Maximum Feret diameter for angles ranging 0 to 180 degrees |
MIN_FERET_ANGLE |
Angle of the minimum Feret diameter |
MAX_FERET_ANGLE |
Angle of the maximum Feret diameter |
STAT_FERET_DIAM_MIN |
Minimum of Feret diameters of the ROI rotated at angles 0-180 degrees |
STAT_FERET_DIAM_MAX |
Maximum of Feret diameters of the ROI rotated at angles 0-180 degrees |
STAT_FERET_DIAM_MEAN |
Mean Feret diameter of the ROI rotated at angles 0-180 degrees |
STAT_FERET_DIAM_MEDIAN |
Median value of Feret diameters of the ROI rotated at angles 0-180 degrees |
STAT_FERET_DIAM_STDDEV |
Standard deviation of Feret diameter of the ROI rotated at angles 0-180 degrees |
STAT_FERET_DIAM_MODE |
Histogram mode of Feret diameters of the ROI rotated at angles 0-180 degrees |
STAT_MARTIN_DIAM_MIN |
Minimum of Martin diameters of the ROI rotated at angles 0-180 degrees |
STAT_MARTIN_DIAM_MAX |
Maximum of Martin diameters of the ROI rotated at angles 0-180 degrees |
STAT_MARTIN_DIAM_MEAN |
Mean of Martin diameter of the ROI rotated at angles 0-180 degrees |
STAT_MARTIN_DIAM_MEDIAN |
Median value of Martin diameters of the ROI rotated at angles 0-180 degrees |
STAT_MARTIN_DIAM_STDDEV |
Standard deviation of Martin diameter of the ROI rotated at angles 0-180 degrees |
STAT_MARTIN_DIAM_MODE |
Histogram mode of Martin diameters of the ROI rotated at angles 0-180 degrees |
STAT_NASSENSTEIN_DIAM_MIN |
Minimum of Nassenstein diameters of the ROI rotated at angles 0-180 degrees |
STAT_NASSENSTEIN_DIAM_MAX |
Maximum of Nassenstein diameters of the ROI rotated at angles 0-180 degrees |
STAT_NASSENSTEIN_DIAM_MEAN |
Mean of Nassenstein diameter of the ROI rotated at angles 0-180 degrees |
STAT_NASSENSTEIN_DIAM_MEDIAN |
Median value of Nassenstein diameters of the ROI rotated at angles 0-180 degrees |
STAT_NASSENSTEIN_DIAM_STDDEV |
Standard deviation of Nassenstein diameter of the ROI rotated at angles 0-180 degrees |
STAT_NASSENSTEIN_DIAM_MODE |
Histogram mode of Nassenstein diameters of the ROI rotated at angles 0-180 degrees |
MAXCHORDS_MAX |
Maximum of ROI’s longest chords built at angles 0-180 degrees |
MAXCHORDS_MAX_ANG |
Angle of the chord referenced in MAXCHORDS_MAX |
MAXCHORDS_MIN |
Minimum of ROI’s longest chords built at angles 0-180 degrees |
MAXCHORDS_MIN_ANG |
Angle of the chord referenced in MAXCHORDS_MIN |
MAXCHORDS_MEDIAN |
Median value of ROI’s longest chords built at angles 0-180 degrees |
MAXCHORDS_MEAN |
Mean value of ROI’s longest chords built at angles 0-180 degrees |
MAXCHORDS_MODE |
Histogram mode of ROI’s longest chords built at angles 0-180 degrees |
MAXCHORDS_STDDEV |
Sndard deviation of ROI’s longest chords built at angles 0-180 degrees |
ALLCHORDS_MAX |
Maximum of all the ROI’s chords built at angles 0-180 degrees |
ALLCHORDS_MAX_ANG |
Angle of the chord referenced in ALLCHORDS_MAX |
ALLCHORDS_MIN |
Minimum of all the ROI’s chords built at angles 0-180 degrees |
ALLCHORDS_MIN_ANG |
Angle of the chord referenced in ALLCHORDS_MIN |
ALLCHORDS_MEDIAN |
Median value of all the ROI’s chords built at angles 0-180 degrees |
ALLCHORDS_MEAN |
Mean value of all the ROI’s chords built at angles 0-180 degrees |
ALLCHORDS_MODE |
Histogram mode of all the ROI’s chords built at angles 0-180 degrees |
ALLCHORDS_STDDEV |
Sndard deviation of all the ROI’s chords built at angles 0-180 degrees |
EULER_NUMBER |
Euler characteristic of the ROI - the number of objects in the ROI minus the number of holes assuming the 8-neighbor connectivity of ROI’s pixels |
EXTREMA_P1_X |
X-ccordinate of ROI’s axis aligned bounding box extremum point #1 |
EXTREMA_P1_Y |
Y-ccordinate of ROI’s axis aligned bounding box extremum point #1 |
EXTREMA_P2_X |
X-ccordinate of ROI’s axis aligned bounding box extremum point #2 |
EXTREMA_P2_Y |
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EXTREMA_P3_X |
X-ccordinate of ROI’s axis aligned bounding box extremum point #3 |
EXTREMA_P3_Y |
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EXTREMA_P4_X |
X-ccordinate of ROI’s axis aligned bounding box extremum point #4 |
EXTREMA_P4_Y |
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EXTREMA_P5_X |
X-ccordinate of ROI’s axis aligned bounding box extremum point #5 |
EXTREMA_P5_Y |
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EXTREMA_P6_X |
X-ccordinate of ROI’s axis aligned bounding box extremum point #6 |
EXTREMA_P6_Y |
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EXTREMA_P7_X |
X-ccordinate of ROI’s axis aligned bounding box extremum point #7 |
EXTREMA_P7_Y |
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EXTREMA_P8_X |
X-ccordinate of ROI’s axis aligned bounding box extremum point #8 |
EXTREMA_P8_Y |
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POLYGONALITY_AVE |
The score ranges from $ -infty $ to 10. Score 10 indicates the object shape is polygon and score $ -infty $ indicates the ROI shape is not polygon |
HEXAGONALITY_AVE |
The score ranges from $ -infty $ to 10. Score 10 indicates the object shape is hexagon and score $ -infty $ indicates the ROI shape is not hexagon |
HEXAGONALITY_STDDEV |
Standard deviation of hexagonality_score relative to its mean |
DIAMETER_MIN_ENCLOSING_CIRCLE |
Diameter of the minimum enclosing circle |
DIAMETER_CIRCUMSCRIBING_CIRCLE |
Diameter of the circumscribing circle |
DIAMETER_INSCRIBING_CIRCLE |
Diameter of inscribing circle |
GEODETIC_LENGTH |
Geodetic length approximated by a rectangle with the same area and perimeter: $ area = geodeticlength * thickness$; $perimeter = 2 * (geodetic_length + thickness) $ |
THICKNESS |
Thickness approximated by a rectangle with the same area and perimeter: $ area = geodeticlength * thickness$; $perimeter = 2 * (geodetic_length + thickness) $ |
ROI_RADIUS_MEAN |
Mean centroid to edge distance |
ROI_RADIUS_MAX |
Maximum of centroid to edge distances |
ROI_RADIUS_MEDIAN |
Median value of centroid to edge distances |
Texture features:
Nyxus feature code |
Description |
|---|---|
GLCM_ANGULAR2NDMOMENT |
Gray Level Co-occurrence Matrix (GLCM) Features, 2nd angular moment |
GLCM_CONTRAST |
GLCM, Contrast |
GLCM_CORRELATION |
GLCM, Correlation |
GLCM_VARIANCE |
GLCM, Variance |
GLCM_INVERSEDIFFERENCEMOMENT |
GLCM, Inverse difference moment |
GLCM_SUMAVERAGE |
GLCM, Sum average |
GLCM_SUMVARIANCE |
GLCM, Sum variance |
GLCM_SUMENTROPY |
GLCM, Sum entropy |
GLCM_ENTROPY |
GLCM, Entropy |
GLCM_DIFFERENCEVARIANCE |
GLCM, Difference variance |
GLCM_DIFFERENCEENTROPY |
GLCM, Difference entropy |
GLCM_INFOMEAS1 |
GLCM, Informational Measure of Correlation (IMC) 1 |
GLCM_INFOMEAS2 |
GLCM, Informational Measure of Correlation (IMC) 2 |
GLRLM_SRE |
Gray level run-length matrix (GLRLM) based feature, Short Run Emphasis |
GLRLM_LRE |
GLRLM, Long Run Emphasis |
GLRLM_GLN |
GLRLM, Gray Level Non-Uniformity |
GLRLM_GLNN |
GLRLM, Gray Level Non-Uniformity Normalized |
GLRLM_RLN |
GLRLM, Run Length Non-Uniformity |
GLRLM_RLNN |
GLRLM, Run Length Non-Uniformity Normalized |
GLRLM_RP |
GLRLM, Run Percentage |
GLRLM_GLV |
GLRLM, Gray Level Variance |
GLRLM_RV |
GLRLM, Run Variance |
GLRLM_RE |
GLRLM, Run Entropy |
GLRLM_LGLRE |
GLRLM, Low Gray Level Run Emphasis |
GLRLM_HGLRE |
GLRLM, High Gray Level Run Emphasis |
GLRLM_SRLGLE |
GLRLM, Short Run Low Gray Level Emphasis |
GLRLM_SRHGLE |
GLRLM, Short Run High Gray Level Emphasis |
GLRLM_LRLGLE |
GLRLM, Long Run Low Gray Level Emphasis |
GLRLM_LRHGLE |
GLRLM, Long Run High Gray Level Emphasis |
GLSZM_SAE |
Gray level size zone matrix (GLSZM) based feature, Small Area Emphasis |
GLSZM_LAE |
Large Area Emphasis |
GLSZM_GLN |
Gray Level Non - Uniformity |
GLSZM_GLNN |
Gray Level Non - Uniformity Normalized |
GLSZM_SZN |
Size - Zone Non - Uniformity |
GLSZM_SZNN |
Size - Zone Non - Uniformity Normalized |
GLSZM_ZP |
Zone Percentage |
GLSZM_GLV |
Gray Level Variance |
GLSZM_ZV |
Zone Variance |
GLSZM_ZE |
Zone Entropy |
GLSZM_LGLZE |
Low Gray Level Zone Emphasis |
GLSZM_HGLZE |
High Gray Level Zone Emphasis |
GLSZM_SALGLE |
Small Area Low Gray Level Emphasis |
GLSZM_SAHGLE |
Small Area High Gray Level Emphasis |
GLSZM_LALGLE |
Large Area Low Gray Level Emphasis |
GLSZM_LAHGLE |
Large Area High Gray Level Emphasis |
GLDM_SDE |
Gray level dependency matrix (GLDM) based feature, Small Dependence Emphasis(SDE) |
GLDM_LDE |
Large Dependence Emphasis (LDE) |
GLDM_GLN |
Gray Level Non-Uniformity (GLN) |
GLDM_DN |
Dependence Non-Uniformity (DN) |
GLDM_DNN |
Dependence Non-Uniformity Normalized (DNN) |
GLDM_GLV |
Gray Level Variance (GLV) |
GLDM_DV |
Dependence Variance (DV) |
GLDM_DE |
Dependence Entropy (DE) |
GLDM_LGLE |
Low Gray Level Emphasis (LGLE) |
GLDM_HGLE |
High Gray Level Emphasis (HGLE) |
GLDM_SDLGLE |
Small Dependence Low Gray Level Emphasis (SDLGLE) |
GLDM_SDHGLE |
Small Dependence High Gray Level Emphasis (SDHGLE) |
GLDM_LDLGLE |
Large Dependence Low Gray Level Emphasis (LDLGLE) |
GLDM_LDHGLE |
Large Dependence High Gray Level Emphasis (LDHGLE) |
NGTDM_COARSENESS |
Neighbouring Gray Tone Difference Matrix (NGTDM) Features, Coarseness |
NGTDM_CONTRAST |
NGTDM, Contrast |
NGTDM_BUSYNESS |
NGTDM, Busyness |
NGTDM_COMPLEXITY |
NGTDM, Complexity |
NGTDM_STRENGTH |
NGTDM, Strength |
Radial intensity distribution features:
Nyxus feature code |
Description |
|---|---|
ZERNIKE2D |
Zernike features |
FRAC_AT_D |
Fraction of total intensity at a given radius |
MEAN_FRAC |
Mean fractional intensity at a given radius |
RADIAL_CV |
Coefficient of variation of intensity within a ring (band), calculated across $n$ slices |
Frequency and orientational features:
Nyxus feature code |
Description |
|---|---|
GABOR |
A set of Gabor filters of varying frequencies and orientations |
2D image moments:
Nyxus feature code |
Description |
|---|---|
SPAT_MOMENT_00 |
Spatial (raw) moments |
SPAT_MOMENT_01 |
of order 00, 01, 02, etc |
SPAT_MOMENT_02 |
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SPAT_MOMENT_03 |
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SPAT_MOMENT_10 |
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SPAT_MOMENT_11 |
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SPAT_MOMENT_12 |
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SPAT_MOMENT_20 |
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SPAT_MOMENT_21 |
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SPAT_MOMENT_30 |
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WEIGHTED_SPAT_MOMENT_00 |
Spatial moments weighted by pixel distance to ROI edge |
WEIGHTED_SPAT_MOMENT_01 |
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WEIGHTED_SPAT_MOMENT_02 |
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WEIGHTED_SPAT_MOMENT_03 |
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WEIGHTED_SPAT_MOMENT_10 |
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WEIGHTED_SPAT_MOMENT_11 |
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WEIGHTED_SPAT_MOMENT_12 |
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WEIGHTED_SPAT_MOMENT_20 |
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WEIGHTED_SPAT_MOMENT_21 |
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WEIGHTED_SPAT_MOMENT_30 |
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CENTRAL_MOMENT_02 |
Central moments |
CENTRAL_MOMENT_03 |
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CENTRAL_MOMENT_11 |
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CENTRAL_MOMENT_12 |
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CENTRAL_MOMENT_20 |
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CENTRAL_MOMENT_21 |
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CENTRAL_MOMENT_30 |
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WEIGHTED_CENTRAL_MOMENT_02 |
Central moments weighted by pixel distance to ROI edge |
WEIGHTED_CENTRAL_MOMENT_03 |
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WEIGHTED_CENTRAL_MOMENT_11 |
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WEIGHTED_CENTRAL_MOMENT_12 |
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WEIGHTED_CENTRAL_MOMENT_20 |
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WEIGHTED_CENTRAL_MOMENT_21 |
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WEIGHTED_CENTRAL_MOMENT_30 |
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NORM_CENTRAL_MOMENT_02 |
Normalized central moments |
NORM_CENTRAL_MOMENT_03 |
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NORM_CENTRAL_MOMENT_11 |
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NORM_CENTRAL_MOMENT_12 |
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NORM_CENTRAL_MOMENT_20 |
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NORM_CENTRAL_MOMENT_21 |
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NORM_CENTRAL_MOMENT_30 |
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NORM_SPAT_MOMENT_00 |
Normalized (standardized) spatial moments |
NORM_SPAT_MOMENT_01 |
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NORM_SPAT_MOMENT_02 |
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NORM_SPAT_MOMENT_03 |
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NORM_SPAT_MOMENT_10 |
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NORM_SPAT_MOMENT_20 |
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NORM_SPAT_MOMENT_30 |
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HU_M1 |
Hu’s moment 1 |
HU_M2 |
Hu’s moment 2 |
HU_M3 |
Hu’s moment 3 |
HU_M4 |
Hu’s moment 4 |
HU_M5 |
Hu’s moment 5 |
HU_M6 |
Hu’s moment 6 |
HU_M7 |
Hu’s moment 7 |
WEIGHTED_HU_M1 |
Weighted Hu’s moment 1 |
WEIGHTED_HU_M2 |
Weighted Hu’s moment 2 |
WEIGHTED_HU_M3 |
Weighted Hu’s moment 3 |
WEIGHTED_HU_M4 |
Weighted Hu’s moment 4 |
WEIGHTED_HU_M5 |
Weighted Hu’s moment 5 |
WEIGHTED_HU_M6 |
Weighted Hu’s moment 6 |
WEIGHTED_HU_M7 |
Weighted Hu’s moment 7 |
Neighbor features:
Nyxus feature code |
Description |
|---|---|
NUM_NEIGHBORS |
The number of neighbors bordering the ROI’s perimeter within proximity radius specified by command line argument –pixelDistance. (Default value of –pixelDistance is 5.) Algorithmically calculating this feature invilves solving the nearest neighbors search problem that in turn involves the proximity measure and the proximity threshold. Particularly, this plugin uses the $L*2$ norm measure over Cartesian space of pixel coordinates and parameter *–pixelDistance_ |
PERCENT_TOUCHING |
Percent of ROI’s contour pixels located at distance 0 from neighboring other ROIs’s contour |
CLOSEST_NEIGHBOR1_DIST |
Distance in pixels from ROI’s centroid to the nearest neighboring ROI’s centroid |
CLOSEST_NEIGHBOR1_ANG |
Angle in degrees between ROI’s centroid and its nearest neighboring ROI’s centroid |
CLOSEST_NEIGHBOR2_DIST |
Distance in pixels from ROI’s centroid to the second nearest neighboring ROI’s centroid |
CLOSEST_NEIGHBOR2_ANG |
Angle in degrees between ROI’s centroid and its second nearest neighboring ROI’s centroid |
ANG_BW_NEIGHBORS_MEAN |
Mean angle in degrees between ROI’s centroid and centroids of its neighboring ROIs |
ANG_BW_NEIGHBORS_STDDEV |
Standard deviation in degrees of angles between ROI’s centroid and centroids of its neighboring ROIs |
ANG_BW_NEIGHBORS_MODE |
Mode value in degrees of angles between ROI’s centroid and centroids of its neighboring ROIs |