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
- 1. The Materials list box
- 2. The Select from list box
- 3. The Add to list box
- 4. The + button
- 5. The - button
- 6. The "D" checkbox, to select fast access tools
- 7. The Fix selection to material check box
- 8. Segmentation tools panel
- 9. The Create button
- 10. The Load button
- 11. The Masked area checkbox
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 Materials list box
The Materials list box shows the names of all materials of the model. When the Show all checkbox is selected all existing materials would be displayed in the Image View panel simultaneously. However, when this checkbox is unchecked the only highlighted material would be shown. Additional context menu is available after selection of material and pressing the right mouse button:
- Rename..., renames the highlighted material
- Set color..., allows setting of a color for the highlighted material. Note! it is also possible to change the colors using the Menu->File->Preferences dialig
- Smooth..., smoothes the selected material of the model with the Gaussian 2D or 3D filter
- Get statistics..., - starts the Statistics dialog to calculate quantification of objects in the selected material of the model Please refer to the Menu->Models->Model statistics... section for details
- Show isosurface (Matlab)..., visualize the highlighted material, as an isosurface. This functionality is powered by Matlab and view3d function written by Torsten Vogel. Use the '*r*' shortcut to rotate and '*z*' to zoom. See more in the Render model... section here.
- Show as volume (Fiji)..., visualization using volume rendering of the selected material of the model with Fiji 3D viewer, please refer to the Microscopy Image Browser System Requirements Fiji for details
- Sync all lists - sets selection in the Material, Select from and Add to lists to the same value
2. The Select from list box
Specifies material for selection. In general use it does not matter which material is selected in this list. However when the Fix selection to material (7.) is checked all selection actions are limited to selected material. It is possible to switch between Exterior (Ext) and any other material with the E shortcut shortcut.
Selection of material in the Select from list and pressing the right mouse button calls a context menu with additional possibilities:
- Set this material as Mask, generates a Mask layer from the selected material. Note! The existing Mask will be erased without confirmation (Press Ctrl+Z for Undo)
- NEW Selection (CURRENT), generates a new Selection layer from the selected material for the currently shown slice
- ADD to Selection (CURRENT), adds the selected material to the Selection layer for the currently shown slice
- Remove Material from Selection (CURRENT), removes the selected material from the Selection layer for the currently shown slice
- NEW Selection (ALL), generates a new Selection layer from the selected material for the whole dataset
- ADD to Selection (ALL), adds the selected material to the Selection layer for the whole dataset
- Remove Material from Selection (ALL), removes the selected material from the Selection layer for the whole dataset
- Sync all lists - sets selection in the Material, Select from and Add to lists to the same value
There are Ctrl+A and Alt+A shortcuts that 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 from | Show Model checkbox | Show Mask checkbox | Result of selection |
All | OFF or ON | OFF | Nothing |
Ext or any material | OFF or ON | OFF | Background or selected material |
Any entry | OFF | ON | Mask |
Any entry | ON | ON | Mask |
The Ctrl+A shortcut will select objects only on the shown slice, while Alt+A will do that for the whole dataset. The selection is sensitive to the Fix selection to material (7.) and the Masked area (11.) switches.
3. The Add to list box
Specifies to which material the selection should be assigned.
For example, material 1 can be selected on all slices (Segmentation Panel->Select from->1, press the Alt+A shortcut) and then copied to the second material 2 (Segmentation Panel->Add to->2, Shift+A). The Shift+A shortcut moves selected areas from the Selection layer to the Model layer, Material 2 for all slices of the dataset. Please refer to the Selection panel reference for more information.
Selection of matirial in the Add to list and pressing the right mouse button calls a context menu with additional possibilities:
- Mask statistics - starts the Statistics dialog to calculate quantification of objects in the Mask layer
- Sync all lists - sets selection in the Material, Select from and Add to lists to the same entry
4. The + button
Press to add a new material to the model.
5. The - button
Press to delete selected in the Select from list box (2.) material from the model.
6. The "D" checkbox, to select fast access tools
Allows to defining of the favorite selection tools that are called using the 'D' key shortcut. The chosen fast access tools are highlighted with orange background in the Selection type popup menu.
7. The Fix selection to material check box
This check box ensures that all segmentation tools (8.) will be performed only for material selected in the Select from list (2.).
8. Segmentation tools panel
This panel hosts different tools for the segmentation. See more here.
9. The Create button
Starts a new model. The existing Model layer will be removed.
10. The Load button
Loads model from the disk. The following formats are accepted:
Alternatively it is possible to use the Menu->Models->Load model .
11. The Masked area checkbox
This check box ensures that all segmentation tools (8.) will be limited only within the masked areas of the image.
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