Segmentation Panel

The segmentation panel is the main panel used for segmentation. It allows creating models, modifying materials and selecting different segmentation tools.

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Contents

What are the Models

Model is a matrix with dimensions equal to those of the opened Image dataset: i.e. [ 1:imageHeight, 1:imageWidth, 1:imageThickness ]. The Model consists of Materials, each element of the Model matrix can belong only to a single material or to an exterior. So it is not possible to have several materials above the same pixel of the Image overlapping each other. Each material in the Model matrix is encrypted with own index:

Model = [1 1 0 0; 1 1 0 0; 0 0 2 2; 0 0 2 2];
Model
Model =

     1     1     0     0
     1     1     0     0
     0     0     2     2
     0     0     2     2

In this example, the shown matrix represents a Model with 2 materials encrypted with 1 (the upper left corner) and 2 (the lower right corner) for the Image of 4x4 pixels.

1. The Segmentation table

The Segmentation table displays the list of materials of the model.

A brief demonstration is available in the following video:
https://youtu.be/_iwQI2DIDjk

The segmentation table has 3 columns:

There Ctrl+A and Alt+A shortcuts can be used. Here is a table with possible results (the Show Model and Show Mask checkboxes are located in the View Settings panel):

Select fromShow Model checkboxShow Mask checkboxResult of selection
AllOFF or ONOFFNothing
Ext or any materialOFF or ONOFFBackground or selected material
Any entryOFFONMask
Any entryONONMask

The Ctrl+A shortcut selects objects only on the shown slice, while Alt+A does that for the whole dataset. The selection is sensitive to the Fix selection to material (4.) and the Masked area (8.) switches.

Programming tips:
Information about selected materials is stored in the UserData field of the segmentation table. It can be obtained using the command:
userData = get(handles.segmTable, 'UserData');

The returned userData structure has fields: If any of these parameters changed the UserData field of the table should be updated:
set(handles.segmTable, 'UserData', userData);

2. The + and - buttons

3. The "D" checkbox, to select fast access tools

This checkbox marks the favorite selection tools that are selected using the 'D' key shortcut. The chosen fast access tools are highlighted with orange background in the Selection type popup menu. Any tool can be selected as a favorite one.

4. The Fix selection to material check box

This check box ensures that all segmentation tools (5.) will be performed only for material selected in the table.

5. Segmentation tools panel

This panel hosts different tools for the segmentation. See more here.

6. The Create button

Starts a new model. The existing Model layer will be removed.

7. The Load button

Loads model from the disk. The following formats are accepted:

Alternatively it is possible to use the Menu->Models->Load model .

8. The Masked area checkbox

This check box ensures that all segmentation tools (5.) will be limited only within the masked areas of the image.

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