The segmentation panel is the main panel used for segmentation. It allows creating models, modifying materials and selecting different segmentation tools.
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 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 (CURRENT) generates a new Selection layer from the selected material for the currently shown slice
- NEW (CURRENT) adds the selected material to the Selection layer for the currently shown slice
- NEW (CURRENT) removes the selected material from the Selection layer for the currently shown slice
- NEW (ALL SLICES) generates a new Selection layer from the selected material for the whole dataset
- NEW (ALL SLICES) adds the selected material to the Selection layer for the whole dataset
- NEW (ALL SLICES) removes the selected material from the Selection layer for the whole dataset
- Material to Mask a copies objects of the selected material to the Mask layer with the options similar to the previous entry
- 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
|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|
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.
Information about selected materials is stored in the UserData field of the segmentation table. It can be obtained using the command:
The returned userData structure has fields:
- prevMaterial - index of selected entry in the Materials column
- prevAddTo - index of selected entry in the Add to column
- showAll - a toggle (0 or 1) to show all or only selected material
- unlink - a toggle (0 or 1) to unlink simultaneous selection of Material and Add to columns
- jScroll - a handle to Java UIScrollPane object
- jTable - a handle to Java UITablePeer object
- the "*+*" button, press to add a new material to the model
- the "*-*" button, press to delete the selected material from the model
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.
This check box ensures that all segmentation tools (5.) will be performed only for material selected in the table.
This panel hosts different tools for the segmentation. See more here.
Starts a new model. The existing Model layer will be removed.
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 .
This check box ensures that all segmentation tools (5.) will be limited only within the masked areas of the image.