Image-Pro Measurements

Measurement Name

Description

Regions:

Area

Area of the pixels under and interior to the boundary.

Area Polygonal Uncalibrated

Area of boundary polygon, without any spatial calibration.

Area Uncalibrated

Count of the pixels under and interior to the boundary.

Area, Polygonal

Area of the polygon defining the region's outline. Same polygon as that used for Perimeter.

Aspect Ratio

Ratio between major axis and minor axis of ellipse equivalent to region.

Axis, Major

Length of major axis of ellipse with same moments of order 0, 1, and 2 as region.

Axis, Minor

Length of minor axis of ellipse with same moments of order 0, 1, and 2 as region.

Bound Box Height

Height of the region's bounding box.

Bound Box Width

Width of the region's bounding box.

Box Area

Ratio between area of region and area of its bounding box.

Box XY

Ratio between width and height of object's bounding box.

Branch Lengths

For each region, the lengths of the Num Dendrites (one-pixel-thick open branches).

Caliper, Max

Longest caliper (Feret diameter) length.

• Number of Angles: Use this sub-setting to set the number of angles (and the size of each angle) over which the caliper is measured.

Caliper, Mean

Mean caliper (Feret diameter) length. Number of Angles: Use this sub-setting to set the number of angles (and the size of each angle) over which the caliper is measured.

• Number of Angles: Use this sub-setting to set the number of angles (and the size of each angle) over which the caliper is measured.

Caliper, Min

Shortest caliper (Feret diameter) length.

• Number of Angles: Use this sub-setting to set the number of angles (and the size of each angle) over which the caliper is measured.

Calipers

Array of NumAngles caliper lengths (Feret diameters)

• Number of Angles: Use this sub-setting to set the number of caliper lengths in the array (and the size of each angle).

Centroid of Mass X

Intensity weighted centroid X-position. Density images (dark regions) must have an intensity calibration.

Centroid of Mass Y

Intensity weighted centroid Y-position. Density images (dark regions) must have an intensity calibration.

Centroid Pixel X

X coordinate of region mean pixel location.  Blob holes are significant (see Centroid to ignore holes).

Centroid Pixel Y

Y coordinate of region mean pixel location.  Blob holes are significant (see Centroid to ignore holes).

Centroid X

X coordinate of the centroid of the region boundary. Blob holes are ignored (see Pixel Centroid X).

Centroid XY

X,Y coordinates of the centroid of the region boundary. Blob holes are ignored.

Centroid Y

Y coordinate of the centroid of the region boundary. Blob holes are ignored (see Pixel Centroid X).

Circularity

Circularity is calculated as the ratio of the area of an object against a circle whose diameter is equal to the object's maximum feret. The value is between 0 and 1.It's calculated as Circ = (4*Area)/(Pi*MaxFeret^2)

Class Number

Class to which region belongs.

Clockwise

Measure of whether a region boundary is drawn clockwise or counterclockwise.

Clumpiness

Fraction of pixels deviating from the average remaining after a dilation, reflecting texture variations.

• Intensity Range Percent: The intensity range as a percentage of the maximum possible intensity range

• Bipolar Pixel Inclusion: Determines which pixels are tested: pixels both sides on the mean intensity, only bright pixels or only dark pixels

• Number of Erosions: The number of 5x5 kernel erosion passes to apply to the heterogeneity mask when computing the clumpiness ratio

Coloc I1

Ratio between colocalized area and the red area above threshold.

Coloc I2

Ratio between colocalized area and the green area above threshold.

Coloc Intersection

Ratio between colocalized area and the total area of the object.

Coloc K1

Overlap coefficient k1. These coefficients describe the differences in intensities of red and green. Simply put, the value k1 is sensitive to differences in intensity for green (second channel) while k2 is sensitive to differences in intensity for red (first channel).

Coloc K2

Overlap coefficient k2. These coefficients describe the differences in intensities of red and green. Simply put, the value k1 is sensitive to differences in intensity for green while k2 is sensitive to differences in intensity for red.

Coloc M1

Colocalization coefficient M1. M1 and M2 estimate the contribution of one color channel in the colocalized areas of the image to the overall colocalized fluorescence in the image. M1 is used to describe the contribution of the second channel (green) to the colocalized area while M2 is used to describe the contribution of the first channel (red). Pixel is considered colocalized if the intensity of the complimentary channel is above the threshold (Thresholds selection mode) or within ROI on colocalization plot (Free ROI selection mode).

Coloc M2

Colocalization coefficient M1. M1 and M2 estimate the contribution of one color channel in the colocalized areas of the image to the overall colocalized fluorescence in the image. M1 is used to describe the contribution of the second channel (green) to the colocalized area while M2 is used to describe the contribution of the first channel (red). Pixel is considered colocalized if the intensity of the complimentary channel is above the threshold (Thresholds selection mode) or within ROI on colocalization plot (Free ROI selection mode).

Coloc M1t

Colocalization coefficient M1t. It represents the total thresholded red intensities that colocalize with thresholded green intensities, divided by total thresholded red intensities.

Coloc M2t

Colocalization coefficient M2t. It represents the total thresholded green intensities that colocalize with thresholded red intensities, divided by total thresholded green intensities.

Coloc Overlap

Overlap coefficient of colocalization.  As Pearson’s Correlation does some averaging of pixel information and can return negative values another method, the Overlap Coefficient, is simultaneously used to describe overlap. This method does not perform any pixel averaging functions, so correlations are returned as values between 0 and 1. This method is not sensitive to intensity variations in the image analysis. This is especially important when considering issues such as camera quantum efficiency, hybridization efficiency and sample photobleaching.

Coloc Pearson

Pearson’s Correlation is a measure of the linear correlation (dependence) between intensities of two channels, giving a value between +1 and −1 inclusive, where 1 is total positive correlation, 0 is no correlation, and −1 is negative correlation. This measure uses only colocalized pixels above colocalization thresholds.

Coloc Pearson All

Pearson’s Correlation of all pixels of the object.

Dendrites, Number of

Number of dendrites (one-pixel-thick open branches).

Dendritic Length

Total length of all the dendrites (one-pixel-thick open branches ).

Diameter of the circle with the same area as the measured object. Calculated as:

Diameter, Max

Length of longest line joining two points of region's outline and passing through the centroid.

Diameter, Mean

Average length of diameters measured at NumAngles intervals and passing through region's centroid.

Diameter, Min

Length of shortest line joining two points of region's outline and passing through the centroid.

Diameters

Array of diameters.

• Number of Angles: Use this sub-setting to set the number of angles in the array (and the size of each angle).

Direction

Angle in degrees of the Major Axis, counterclockwise from the horizontal.

Fourier Descriptor

FFT spectrum of the outline. Translation, Scale and Rotation invariant shape measurement.

Fractal Dimension

Fractal dimension of the region's outline.

Heterogeneity

Fraction of pixels that deviate more than the IntensityRange (10% default) from the average intensity.

• Intensity Range Percent: The intensity range as a percentage of the maximum possible intensity range.

• Bipolar Pixel Inclusion: This setting determines which pixels are tested. Pixels on both sides of the mean intensity, only bright pixels or only dark pixels.

Hole Area

Area of the holes within the region.

Hole Area Ratio

Ratio of region area excluding holes to total area of region.

Hole Indices

For each region, an array of NumHole hole indices.

Hole Parent Index

If a hole, parent feature index, -1 if not a hole.

Holes, Number of

Number of holes within the region.

Ill-Formed Boundary

Ill-formed boundary: 0 OK, 1 non-convex, 2 minor double-valued, 3 major double-valued, 4 zero area segment(s), 5 centroid outside, 6 self-crossing.

Integrated OD

Integrated Optical Densisty (or integrated intensity). Computed as Pixel Area times Mean Intensity.

Integrated OD Blue

Integrated Optical Densisty (or integrated intensity) for the Blue channel of color images. Computed as Pixel Area times  Intensity Blue.

Integrated OD Green

Integrated Optical Densisty (or integrated intensity) for the Green channel of color images. Computed as Pixel Area times  Intensity Green.

Integrated OD Red

Integrated Optical Densisty (or integrated intensity) for the Red channel of color images. Computed as Pixel Area times  Intensity Red.

integrated OD Uncalibrated

Uncalibrated Integrated Optical Densisty (or integrated intensity). Computed as Pixel Area Uncalibrated times Mean Intensity Uncalibrated.

Intensity Blue

Region's mean blue value. Color images only.

Intensity Green

Region's mean green value. Color images only.

Intensity Red

Region's mean red value. Color images only.

Intensity Uncalibrated

Average uncalibrated luminance (Intensity or Optical Density) of region.

Intensity, Max

Maximum luminance (intensity or density) inside region.

Intensity, Mean

Average calibrated luminance (Intensity or Optical Density) of region.

Intensity, Min

Minimum luminance (intensity or density) inside region.

Intensity, Std Dev

Standard deviation of the luminance (intensity or density) inside region.

Lab color a

CIE L*a*b* color component a, green–red.

Lab color b

CIE L*a*b* color component b, blue–yellow.

Lab color L

CIE L*a*b* color component L, lightness.

Length

Caliper length (i.e. Feret diameter) along major axis of region.

Margination

Relative distribution of region intensity between the center and margin, with larger values from brighter centers. A value of 0.33 indicates a homogenous region.

Nest Parent Index

Parent feature index for nested regions, -1 for outer-most regions.

Nested Child Indices

For each region, an array of feature indices of its immediate nested children.

Nested Children Count

Number of nested immediate child features.

Nesting Depth

Nesting depth (outer-most regions have zero depth) .

Percent Area (%)

Ratio of area of region to total area of image or ROI in percents (range from 0 to 100).

Percent Area (Ratio)

Ratio of area of region to total area of image or ROI.

Percent Area Parent

Area of the object in percents of the parent object area. If the object doesn't have parent, the whole image is used as parent.

Perimeter Ratio

Convex perimeter / Perimeter (max value of 1.0)

Perimeter Uncalibrated

Perimeter of boundary polygon, without any spatial calibration.

Perimeter, Bounding Pixels

Chain code length of the outline. Faster but less accurate than Perimeter.

Perimeter, Bounding Polygon

Length of the region's boundary. More accurate than the Pixel Perimeter.

Perimeter, Convex Hull

Perimeter of the convex outline of the region.

Perimeter, Equiv. Ellipse

Perimeter of the region's equivalent ellipse.

The average intensity of all child objects found within a parent object. This measurement can only be used as part of a protocol.

Protocols

The integrated Optical Density of the feature in the original monochrome channel. This measurement can only be used as part of a protocol.

Protocols

The maximum intensity of the feature in the original monochrome channel. This measurement can only be used as part of a protocol.

Protocols

The average intensity of the feature in the original monochrome channel. This measurement can only be used as part of a protocol.

Protocols

The minimum intensity of the feature in the original monochrome channel. This measurement can only be used as part of a protocol.

Protocols

The total length of all the child objects found within a parent object. This measurement can only be used as part of a protocol.

Protocols

The total number of child objects found within a parent object. This measurement can only be used as part of a protocol.

Protocols

Radii

Array of radii.

• Number of Angles: Use this sub-setting to set the number of angles in the array (and the size of each angle).

Radius Ratio

Ratio between Maximum Radius and Minimum Radius.

Radius, Max

Maximum distance between region centroid and boundary.

Radius, Min

Minimum distance between region centroid and boundary.

Relative Size

Size as an integral multiple of the size of the smallest selected regions.

• Relative Size Override: The reference size in square calibrated units. If zero, the average size of small objects is the reference size.

• Float Results: When checked, the results are relative size ratio, if unchecked, the results are the clustering count.

Roundness

A measure of roundness (perimeter^2)/(4.pi.area).

Saturation

Saturation of the color object calculated from average RGB values.

Size Count

Size weighted region "count". It must be used with Clean Borders options set to All. The measurement reports the probability of the object been not discarded by Clean borders filter. The value range is from 0 to 1, where small objects have values close to 1 and large, comparable with the image size, close to 0.

Volume of the sphere with the equivalent diameter of the measured object. Calculated as:

where D- Diameter, Equivalent Circle

Width

Caliper length (i.e. Feret diameter) along minor axis of region.

YIQ color I

I component of YIQ color space, chrominance in orange-blue range.

YIQ color Q

Q component of YIQ color space, chrominance in purple-green range.

YIQ color Y

Y component of YIQ color space, Luma, corresponds to weighted Gray intensity.

Lines:

Angle

Angle counterclockwise from the horizontal, in degrees.

Arc Angle

Angle of best-fit arc created from each feature. Angle is calculated from the start point of the line in counterclockwise direction.

Arc Center X

Center X of best-fit arc created from each feature.

Arc Center Y

Center Y of best-fit arc created from each feature.

Arc Radius

Radius of best-fit arc created from each feature.

Chord Length

Chord (start to end) line length.

Chord Ratio

Ratio of the Chord Length to the total Length.

End X

X coordinate of the end of the line.

End XY

X,Y coordinates of the end of the line.

End Y

Y coordinate of the end of the line.

Length

Total length of the line.

Length Uncalibrated

Total length of the line without any spatial calibration.

Position X

X coordinate of the mean position of the line.

Position XY

X,Y coordinates of the mean position of the line.

Position Y

Y coordinate of the mean position of the line.

Segment Count

Count of polyline segments (always 1 for simple lines).

Start X

X coordinate of the start of the line.

Start XY

X,Y coordinates of the start of the line.

Start Y

Y coordinate of the start of the line.

Points:

Intensity

Calibrated image luminance (density or intensity) at the point.  Value is interpolated for points falling between pixels.

Intensity Uncalibrated

Uncalibrated image luminance at the point.  Value is interpolated for points falling between pixels.

Location X

X location of the point.

Location XY

X,Y location of the point.

Location Y

Y location of the point.

Best Fit:

Max Distance

Maximum distance between object and best-fit points

Mean Distance

Average distance between object and best-fit points

Min Distance

Minimum distance between object and best-fit points

RMSE

Root Mean Squared Error of distance between object and best-fit points

Objects:

Class

Class of object

Class Name

Class name of object

Parent

Name of the parent object

Measurement Name

Description

Volumes:

Angle Alpha

Angle between surface normal and reference vector.

Angle Gamma

Angle between projection of surface normal to the direction plane and the direction vector.

Angle Norm dev

Deviation of normal vectors on surface. Zero for flat surface, 1.336 for circle.

Angle Theta

Angle between the Reference vector and the projection of the normal to the plane perpendicular to the Direction vector.

Angle X

Angle between longest object line and axis X.

Angle Y

Angle between longest object line and axis Y.

Angle Z

Angle between longest object line and axis Z.

Area

Area of the closed polyline calculated as a sum of areas of triangles

Area of Surface

Surface area of object in calibrated units

Box ratio

Ratio between maximum and minimum size of the bounding box. R = Max / Min

Box volume

Volume of object's bounding box  ( V = W * H * D )

Box Volume fraction

Ratio of object's volume to the box volume R = Vobj / Vbox

Center of Mass X

X coordinate of center of mass. The parameter is calculated using optical density of voxels.

Center of Mass Y

Y coordinate of center of mass. The parameter is calculated using optical density of voxels.

Center of Mass Z

Z coordinate of center of mass. The parameter is calculated using optical density of voxels.

Center X

X coordinate of the center of object

Center Y

Y coordinate of the center of object

Center Z

Z coordinate of the center of object

Coloc I1

Ratio between colocalized area and the red area above threshold.

Coloc I2

Ratio between colocalized area and the green area above threshold.

Coloc Intersection

Ratio between colocalized area and the total area of the object.

Coloc K1

Overlap coefficient k1. These coefficients describe the differences in intensities of red and green. Simply put, the value k1 is sensitive to differences in intensity for green (second channel) while k2 is sensitive to differences in intensity for red (first channel).

Coloc K2

Overlap coefficient k2. These coefficients describe the differences in intensities of red and green. Simply put, the value k1 is sensitive to differences in intensity for green while k2 is sensitive to differences in intensity for red.

Coloc M1

Colocalization coefficient M1. M1 and M2 estimate the contribution of one color channel in the colocalized areas of the image to the overall colocalized fluorescence in the image. M1 is used to describe the contribution of the second channel (green) to the colocalized area while M2 is used to describe the contribution of the first channel (red). Pixel is considered colocalized if the intensity of the complimentary channel is above the threshold (Thresholds selection mode) or within ROI on colocalization plot (Free ROI selection mode).

Coloc M2

Colocalization coefficient M1. M1 and M2 estimate the contribution of one color channel in the colocalized areas of the image to the overall colocalized fluorescence in the image. M1 is used to describe the contribution of the second channel (green) to the colocalized area while M2 is used to describe the contribution of the first channel (red). Pixel is considered colocalized if the intensity of the complimentary channel is above the threshold (Thresholds selection mode) or within ROI on colocalization plot (Free ROI selection mode).

Coloc M1t

Colocalization coefficient M1t. It represents the total thresholded red intensities that colocalize with thresholded green intensities, divided by total thresholded red intensities.

Coloc M2t

Colocalization coefficient M2t. It represents the total thresholded green intensities that colocalize with thresholded red intensities, divided by total thresholded green intensities.

Coloc Overlap

Overlap coefficient of colocalization.  As Pearson’s Correlation does some averaging of pixel information and can return negative values another method, the Overlap Coefficient, is simultaneously used to describe overlap. This method does not perform any pixel averaging functions, so correlations are returned as values between 0 and 1. This method is not sensitive to intensity variations in the image analysis. This is especially important when considering issues such as camera quantum efficiency, hybridization efficiency and sample photobleaching.

Coloc Pearson

Pearson’s Correlation is a measure of the linear correlation (dependence) between intensities of two channels, giving a value between +1 and −1 inclusive, where 1 is total positive correlation, 0 is no correlation, and −1 is negative correlation. This measure uses only colocalized pixels above colocalization thresholds.

Coloc Pearson All

Pearson's Correlation of all pixels of the object.

Density (max)

Maximum density of object.

Density (mean)

Mean density of object

Density (min)

Minimum density of object.

Density (st.dev.)

Standard deviation of optical density of object

Density Blue

Average density blue of colocalized object.

Density Green

Average density green of colocalized object.

Density IOD

Integrated Optical Density of object

Density Red

Average density red of colocalized object.

Depth

Size of bounding box in Z direction

Diameter

Equivalent diameter of object

Feret (max)

Maximum distance between two parallel planes enclosing object.

Feret (min)

Minimum distance between two parallel planes enclosing object.

Feret Ratio

Ratio between Feret (max) and Feret (min).

Height

Size of bounding box in Y direction

Hole Count

Number of 3D holes in the object.

Hole Ratio

Ratio between total volume of holes to volume of the object.

Hole Volume

Total volume of 3D holes in the object.

Parent Name

Name of the parent object.

Parent Object ID

Object ID of the parent. 0 - no parent.

Percent Volume Parent

Volume percentage of the object relatively to the volume of the parent.

Points

Number of points in polyline

Radius (max)

Maximum distance between object's centroid and surface

Radius (min)

Minimum distance between object's centroid and surface

Radius Ratio

Ratio between Radius (max) and Radius (min)

Sphericity

Sphericity of object, calculated as 6 volumes of object divided by equivalent diameter and surface area of object. For a spherical objects this parameter equals 1, for all other shapes it is less than 1.

Surface ID

Index of parent iso-surface.

Surface Name

Name of parent iso-surface.

Volume

Volume of object in calibrated units

Volume Percentage

Percentage of the object volume in the whole volume.

Width

Size of bounding box in X direction

Lines:

Angle

Angle value

Area

Area of the closed polyline calculated as a sum of areas of triangles

Center X

Center X of object

Center Y

Center Y of object

Center Z

Center Z of object

End X

X coordinate of the end point

End Y

Y coordinate of the end point

End Z

Z coordinate of the end point

Length

Total length of line segments

Points

Number of points in polyline

Start X

X coordinate of the starting point

Start Y

Y coordinate of the starting point

Start Z

Z coordinate of the starting point

Objects:

Class

Class to which object belongs. The classification can be done using the Histogram window.