Statistics for Mask or Model objects
This dialog provides access to statistic values for shapes and intensities for model and mask objects.
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Contents
Parameters and Options
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- 10. A histogram plot that shows distribution of statistic parameters from 8.. The plot may be shown on a normal or logarithmic scale depending on selection of the Log scale check box (13.). Clicks with the left and right mouse allows to make selections.
- 11. The Auto highlight on a click checkbox - when checked, each time the object in the table (8.) is selected it is highlighted in the Image View panel.
- 12. The Log scale checkbox is for showing the histogram (8.) in the logarithmic scale.
- 13. Two edit boxes are used to provides minimal and maximal values for highlighting after press of the Do button.
- 14. The Run button starts quantification.
- 15. The Details panel defines a way of object selection: the selected objects may be added, removed or used for replacement of the Selection layer.
- 16. The Export button allows export of the statistic values to Excel or Matlab.
- 17. The Sort button sorts the main table values; use a popup menu via the right mouse button to define a column to be sorted.
Statistical properties of 3D objects
Calculate properties of 3D objects of the dataset.
- Area - calculates total number of pixels (~volume) within the 3D objects.
- Endpoints Length - calculates the distance between two end points of a line segment. Please note that the width of the line should be 1. It is recommended to use Membrane ClickTracker tool in the Segmentation panel with the option Straight line and Width=1. Note! The resulting numbers are calculated in the image units.
- EquatorialEccentricity - returns the Equatorial Eccentricity, defined as the eccentricity of the section through the second longest and the shortest axes. The resulted values between 1 (line) and 0 (sphere)
- FilledArea - calculates total number of pixels (~volume) within the filled 3D objects.
- Holes Area - finds cavities within 3D objects and calculate their total number of pixels (~volume).
- MajorAxisLength - returns the length of the major axis in pixels
- MeridionalEccentricity - returns Meriodional Eccentricity, defined as the eccentricity of the section through the longest and the shortest axes
- SecondAxisLength - returns the length of the second major axis in pixels
- ThirdAxisLength - returns the length of the minor axis in pixels
Statistical properties of 2D objects
Calculate properties of 3D objects of the dataset.
- Area - calculates total number of pixels within the 2D objects.
- ConvexArea - calculates total number of pixels of the smallest convex polygon that can contain the object.
- CurveLengthInPixels - calculate the length of curve objects in pixels. It is possible to measure the length of both closed and non-closed curves. Please note! It is required that the curves are thinned (Menu->Selection->Morphological operations) and the branch points are removed (The branch points may be found by selecting material and run branch point detection, Menu->Selection->Morphological operations|).
- CurveLengthInUnits - calculates the length of curved objects in physical units of the dataset. It is possible to measure the length of both closed and non-closed curves. Please note! It is required that the curves are thinned (Menu->Selection->Morphological operations) and the branch points are removed (The branch points may be found by selecting material and run branch point detection, Menu->Selection->Morphological operations|).
- Eccentricity - calculates eccentricity of the ellipse that has the same second-moments as the object. The eccentricity is the ratio of the distance between the foci of the ellipse and its major axis length. The value is between 0 and 1. (0 and 1 are degenerate cases; an ellipse whose eccentricityis 0 is actually a circle, while an ellipse whose eccentricity is 1 is a line segment.)
- Endpoints Length - calculates the distance between two end points of a line segment. Please note that the width of the line should be 1. It is recommended to use Membrane ClickTracker tool in the Segmentation panel with the option Straight line and Width=1. If the lines were drawn with the Brush tool they have to be thinned. The thinning may be achieved with the Brush tool size 1 or/and Thinning the objects using Menu->Selection->Morphological 2D operations->Thin. Note! The resulting numbers are calculated in the image units.
- EquivDiameter - calculates the diameter of a circle with the same area as the object. Computed as sqrt(4*Area/pi).
- EulerNumber - calculates the number of objects in the region minus the number of holes in those objects, i.e. the object with 1 hole has the Euler number 0, while the object with 2 holes has the Euler number -1.
- Extent - calculates the ratio of pixels in the object to pixels in the total bounding box. Computed as the Area divided by the area of the bounding box.
- FilledArea - calculates the number of pixels of the filled object.
- Holes Area - finds holes and calculates total number of pixels within them.
- MajorAxisLength - calculates the length (in pixels) of the major axis of the ellipse that has the same normalized second central moments as the object.
- MinorAxisLength - calculate the length (in pixels) of the minor axis of the ellipse that has the same normalized second central moments as the object.
- Orientation - calculates the angle (in degrees ranging from -90 to +90 degrees) between the x-axis and the major axis of the ellipse that has the same second-moments as the object.
- Perimeter - calculates the distance around the boundary of the object. It is computed as the perimeter by calculating the distance between each adjoining pair of pixels around the border of the region.
- Solidity - calculates the proportion of the pixels in the convex hull that are also in the object. Computed as Area/ConvexArea.
Statistical properties of intensities of 2D/3D objects
These properties are calculated when the Intensity radio button in the Mode panel (3.) is selected.
- MinIntensity - detects minimal value of the image intensity within 2D or 3D objects.
- MaxIntensity - detects maximal value of the image intensity within 2D or 3D objects.
- MeanIntensity - calculates average intensity of the image within 2D or 3D objects.
- StdIntensity - calculates standard deviation intensity of the image within 2D or 3D objects.
- SumIntensity - calculates sum of the image intensities within 2D or 3D objects.
- Correlation - calculates correlation between image intensities of the two selected color channels. See more in the help of Matlab corr2 function.
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