The segmentation panel is the main panel used for segmentation. It allows creating models, modifying materials and selecting different segmentation tools.
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.
The Create button
Starts a new model. The existing Model layer will be removed.
Whenever is possible is is recommended to use models with 63
A short introduction about materials with more than 255 materials is available from here:
Also see more about types of model on the Menu->Models page
The Load button
Loads model from the disk. The following formats are accepted:
- Matlab (*.MAT), default recommended format
- Amira Mesh binary (*.AM); for models saved in Amira format
- Hierarchial Data Format (*.H5); for data exchange with Ilastik
- Medical Research Concil format (*.MRC); for data exchange with IMOD
- NRRD format (*.NRRD); for models saved in 3D slicer format
- TIF format (*.TIF);
- Hierarchial Data Format with XML header (*.XML);
- all standard file formats can be opened when selecting "All files(.)"
Alternatively it is possible to use the Menu->Models->Load model or directly drag-and-drop *.model file to the Image View panel.
The +, -, and E buttons
- the "*+*" button, press to add a new material to the model (only for models with 63 and 255 materials)
- the "*-*" button, press to delete the selected material from the model (only for models with 63 and 255 materials)
- the "*E*" button, press to find and select the next empty index in the model (only for models with more than 255 materials)
The Filled/Contour combo box
This combo box modifies visualization of materials in the Image View panel.
- Filled - use to draw materials as the filled shapes (faster)
- Contour - use to draw only the contours of materials (slower)
The Segmentation table
The Segmentation table displays the list of materials of the model.
A brief demonstration is available in the following video:
The segmentation table has 3 columns:
- Column "C" shows the colors for each material. The mouse click on the first column starts a dialog for color selection
- Colimn "Material" has a list of all materials. The right mouse click starts a popup menu with additional options for the selected material:
- Show selected material only a toggle that switches visualization of materials in the Image View panel, when checked only the selected material is shown
- Rename rename the selected material
- Set color change color for the selected material
- Get statistics calculate properties for objects that belong to the selected material. Please refer to the Menu->Models->Model statistics... section for details
- Material to Selection a copies objects of the selected material to the Selection layer with the following options:
- NEW (2D, Slice) generates a new Selection layer from the selected material for the currently shown slice
- ADD (2D, Slice) adds the selected material to the Selection layer for the currently shown slice
- REMOVE (2D, Slice) removes the selected material from the Selection layer for the currently shown slice
- NEW (3D, Stack) generates a new Selection layer from the selected material for the current stack
- ADD (3D, Stack) adds the selected material to the Selection layer for the current stack
- REMOVE (3D, Stack) removes the selected material from the Selection layer for the current stack
- NEW (4D, Dataset) generates a new Selection layer from the selected material for the whole dataset
- ADD (4D, Dataset) adds the selected material to the Selection layer for the whole dataset
- REMOVE (4D, Dataset) removes the selected material from the Selection layer for the whole dataset
- Material to Mask copy the selected material to the Mask layer with the options similar to Material to Selection section
- Mask to Material copy the Mask layer to the selected material with the options similar to Material to Selection section
- Show as volume (MIB).. visualize the selected material using MIB rendering, available for Matlab R2018b and newer
- Show isosurface (Matlab)... visualize the model or only the selected material (when Show selected material only is selected), 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
- Show as volume (Fiji)... visualization of the model or selected material (when Show selected material only is selected) using volume rendering with Fiji 3D viewer, please refer to the Microscopy Image Browser System Requirements Fiji for details
- Unlink material from Add to when unlinked, the Add to column is not changing its status during selection of Materials
- Column "Add to" defines destination material for the Selection layer during the Add and Replace actions. By default, this field is linked to the selected material, but it is unlinked when the Fix selection to material checkbox is selected or the Unlink material from Add to option is enabled
The Ctrl+A and Alt+A shortcuts can be used to highlight selected in the Segmentation table material. 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 and the Masked area switches.
- To select a combination of the Mask and any other layer:
- select the Mask entry in the table
- check the Fix selection to material checkbox
- select the second material in the Add to column
- Press the Alt+A or Ctrl+A shortcut
The Fix selection to material check box
This check box ensures that all segmentation tools will be performed only for material selected in the table.
The Masked area checkbox
This check box ensures that all segmentation tools will be limited only within the masked areas of the image.
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.
Segmentation tools combo box
This combo box hosts different tools for the segmentation. See more here.