Statistics for Mask or Model objects

This dialog provides access to statistic values for shapes and intensities for model and mask objects.

Back to Index --> User Guide --> Menu --> Models Menu --- Mask Menu

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Parameters and Options
Statistical properties of 3D objects
Statistical properties of 2D objects
Statistical properties of intensities of 2D/3D objects

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Parameters and Options

The Objects panel - using combo boxes of this panel it is possible to select material for analysis and type of the dataset: current slice (2D Slice), current Z-stack (3D Stack) or for the whole volume (4D Dataset).
For the models with more than 255 materials the upper combo box has a 'Model' option. When this option is used, the tool quantifies all materials of the model at once; as result each material is described with a single value
The Shape panel - allows selection of type of objects to detect: |2D| or |3D|
3The Mode panel - when the Object mode is selected the dialog returns statistic that is based on shape properties of objects, otherwise (Intensity mode) based on image intensities behind the objects

Properties to detect. Note! The EndpointsLength requires the objects to be lines with diameter of 1 pixel; in addition, the 8/26 connectivity should be selected. See below for available properties to measure
Connectivity parameter is used for separation of objects. The connectivity 4/6 means that the objects that are touching eachother at the corners will be separated into two individual objects
The first color channel combobox is used to specify color channel for image intensity analysis
The second color channel combobox for correlation intensity analysis
The Units combobox specify units for the results: pixels or physical units.

Additional info

Important! some parameters can only be calculated in pixels;
in addition, calculation of certain properties (such as MeridionalEccentricity, EquatorialEccentricity, MajorAxisLength, SecondAxisLength, ThirdAxisLength, EquivDiameter, Surface Area) of 3D objects in physical units is correct only for isotropic voxels

The [✓] *multiple properties checkbox* allows detection of several object properties at the same time. The properties can be selected using the Define properties button

Available properties for calculation

The Statistics table contains calculated values. The objects in this window may be sorted (see below) or selected. Please press the right mouse button button for a context menu with selection parameters.

Context menu for the Statistics table

Context menu entry	Description
New selection	Makes new selection based on the highlighted objects
Add to selection	Adds highlighted objects to the selection
Remove from selection	Removes highlighted objects from the selection
Copy column(s) to clipboard	Copy the content of the highlighted column(s) to the system clipboard
New annotations	Makes a new annotation list: adds a label to the selected objects. The annotations can be accessed via Menu->Models->Annotations or Segmentation panel->Selection type->Annotations
Add to selection	Adds highlighted objects to the annotation list
Remove from annotations	Removes highlighted objects from the annotation list
Calculate Mean	Calculates average value of the highlighted objects and copy it into clipboard
Calculate Sum	Calculates sum of the highlighted objects and copy it into clipboard
Calculate Min	Calculates minimal value of the highlighted objects and copy it into clipboard
Calculate Max	Calculates maximal value of the highlighted objects and copy it into clipboard
Crop to a file/matlab	Crops the dataset based on detected 3D objects. It is possible to add margins during the crop and crop both Model and Mask layers. The results can be saved to a file or exported to MATLAB Parameters Target: where to crop the objects MarginXY: extend the bounding box around the object by the specified number of pixels MarginZ: extend the bounding box around the object by the specified number of pixels in the Z dimension Jitter XY centroids use this option to introduce a random jitter of XY coordinates. This jitter will shift the crop window left/right/up/down randomly depending on the provided value in the Variation edit box. The random generator is initialized using the Seed edit box. When seed is 0 a random value used to initalize the random generator. When any other number is used, that number is initializing the random generator Crop Model: also include cropping of the model Crop Mask: also include cropping of the mask Single Mask object per dataset: keep only a main object in the crop of the Mask, enabled only when the objects were identified from the mask layer The data is exported to MATLAB as a structure [Filename_IndexOfTheObject] with the following fields: .img - cropped image [1:height, 1:width, 1:colors, 1:stacks] .meta - meta data for the cropped image [1:height, 1:width, 1:colors, 1:stacks] .Model - a structure with the Model, including .model, .modelMaterialNames, .modelMaterialColors fields .labelText - cell array with annotations .labelPosition - a matrix with coordinates for the annotations [z, x, y] .Mask - a matrix with the Mask layer [1:height, 1:width, 1:stacks] that corresponds to the cropped image The exported data can be imported back to MIB using the `Menu->File->Import image from...->MATLAB` and providing variables to import, for example Filename_IndexOfTheObject.img and Filename_IndexOfTheObject.meta. Or for the Model: Menu->Models->Import model from MATLAB-> and providing variable with the model, for example Filename_IndexOfTheObject.Model.
Objects to a new model	Generate a new model, where each of the selected objects will be assigned to an own index https://youtu.be/xZhuv659JrY
Plot histogram	Draws a histogram bar plot from the selected data

Histogram plot shows distribution of statistic parameters from the Statistics table. The plot may be shown on a normal or logarithmic scale depending on selection of the Log scale check box. Clicks with the left and right mouse button allows to make selections.
The [✓] Auto highlight on a click checkbox - when checked, each time the object in the Segmentation table is selected it is highlighted in the Image View panel
The Sorting combobox can be used to change the sorting of the main table
The [✓] Log scale checkbox is for showing the histogram in the logarithmic scale
Two edit boxes are used to provides minimal and maximal values for highlighting after press of the Do button.
The Run button starts quantification.
The Details panel defines a way of object selection: the selected objects may be added, removed or used for replacement of the Selection layer.
The Export button allows export of the statistic values to Excel or MATLAB.

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Statistical properties of 3D objects

Calculate properties of 3D objects of the dataset.

List of 3D properties

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

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Statistical properties of 2D objects

Calculate properties of 3D objects of the dataset.

List of 2D properties

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.
FirstAxisLength - length of the major 2D axis of the object, in contrast to MajorAxisLength this property returns the real length of the object rather than that for the ellipse
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
SecondAxisLength - length of the minor 2D axis of the object, in contrast to MinorAxisLength this property returns the real length of the object rather than that for the ellipse
Solidity - calculates the proportion of the pixels in the convex hull that are also in the object. Computed as Area/ConvexArea.

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Statistical properties of intensities of 2D/3D objects

These properties are calculated when the Intensity radio button in the Mode panel is selected.

List of intenstity properties

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.

Back to Index --> User Guide --> Menu --> Models Menu --- Mask Menu

Statistics for Mask or Model objects

Contents

Parameters and Options

Statistical properties of 3D objects

Statistical properties of 2D objects

Statistical properties of intensities of 2D/3D objects