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

Contents

Parameters and Options

  • 1. 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
  • 2. The Shape panel - allows selection of type of objects to detect: |2D| or |3D|
  • 3. The 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
  • 4. Select 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
  • 5. Define connectivity parameter that will be 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
  • 6. The first color channel combobox is used to specify color channel for image intensity analysis
  • 7. The second color channel combobox for correlation intensity analysis
  • 8. The Units combobox specify units for the results: pixels or physical units. 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
  • 8. The multiple properties checkbox allows detection of several object properties at the same time. The properties can be selected using the Define properties button
  • 9. The Statistics table contains calculated values. The objects in this window may be sorted (*16.*) or selected. Please press the right mouse button button for a context menu with selection parameters:
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
  • 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

Statistical properties of 3D objects

Calculate properties of 3D objects of the dataset.

Statistical properties of 2D objects

Calculate properties of 3D objects of the dataset.

Statistical properties of intensities of 2D/3D objects

These properties are calculated when the Intensity radio button in the Mode panel (3.) is selected.

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