- File: enables to reload, save and rename an object.
- Color: enables to change the object color. Sub menus can be : palette, material and texture. See the section called “Objects color”
- Referential: enables to change the object referential. See the section called “Referentials and transformations in Anatomist”
- ROI: create an associated ROI graph. See Chapter 9, ROI drawing toolbox to read how to draw Regions of Interest.
- Volume rendering: use transparency to render the whole volume in a 3D window. Different tissues (or grey levels) may be assigned different opacities and colors to make them appear in 3D or disapear.
- Geometry
- Landmarks
- Display: enables to display all nodes or edges.
- Labelling
- Landmarks
- ROI
Colors can be changed for several objects types, including: volume, texture, mesh, bucket and graph nodes. According to the object type, colors are changed by different methods:
Mesh: Material modification.
Texture: Texturing and Palette modification.
Volume: Palette, Texturing and Material modification. Palette is the most commonly used. But a volume is also considered as a geometric object (a mesh representing a rectangle) with values (texture) associated to each point. So by extension, volumes have acces to mesh (Material) and texture (Texturing) menus.
Textured object (obtained by mesh and texture fusion): Texturing modification.
The palette allows to change the color aspect of the texture part of objects. Choose Color => Palette in Object-specific menu or by right-click on the object
In medical imaging, we generally use 3D (or 4D) volumes of scalar values: each voxel represents a scalar value (or a grey level). Grey levels may be associated to colors via a palette. A palette is a table that associates colors to voxels values. Anatomist palettes can be modified using the values min (minimum value for the voxels of the volume) and max (maximum value for the voxels of the volume). Changing these boundaries modifies the field of voxels values where the palette applies. So one may "zoom" on a part of the histogram. The same applies to scalar textures mapped on a mesh.
The min and max boundaries of the palette can also be changed directly in the visualization window without opening the palette menu. The following keyboard shortcuts can be used to do so:
- CTRL key + Right clic button and move the mouse up and down: changes the max boundary
- CTRL key + Right clic button and move the mouse left and right: changes the min boundary
A number of palettes are available and any user can add his own personal palettes.
Note
The default palette for a volume is B-W LINEAR, and Min and Max bounds are set so that they contain 99% of histogram values. The default palette for a mesh texture is a Blue-Red gradient.RGB and RGBA volumes do not have any palette yet.
Some textures are 2D: each mesh vertex has 2 different texture values, which may be interpreted as a 2D coordinate on a palette image. For this it is possible to use a 2D image as a palette, or to mix two 1D palettes.
Table 5.2. Palette parameters
| Champ | Description |
|---|---|
| Available palettes | List of available palettes. You can add your own palettes. |
| Update mode | Display update : to have a real time update, check the box Responsive. Else uncheck it and click on the button Update to update display. |
| Dimension |
1D : the palette is considered as a line : a value of voxel is associated to a point (x) of the palette. 2D : the palette is considered as a 2D image : a value of voxel is associated to a point (x, y) of the palette. You can choose a 2D palette in the list of palettes (eg : blue-red-black-dark) or composed one from two 1D palettes. |
| Min | Associates the first color of the palette to a voxel or texture value: any voxel which has a value inferior to this value will be associated to the first color of the palette. |
| Max | Associates the first color of the palette to a voxel or texture value: any voxel which has a value superior to this value will be associated to the last color of the palette. |
| Bounds | These are the min and max values of the graphical min/max sliders just above. |
| Reset values | Sets automatically computed values for min and max (take into account 99% of the histogram values). |
| Reset bounds | Reset the bounds : min = minimum value of the volume voxels and max = maximum value of the volume voxels. |
| Palette view | View of the palette according to the choosen min, max and bounds. It represents the colors distribution on the object. |
| Use a second palette for 2D | Check it if you want to compose a 2D palette from two 1D palettes (only useful for 2D textures). |
| Second palette | List of available palettes. |
| Palettes mixing method | Choose the palettes mixing method geometric fusion or linear. |
| Palette 1D mapping : FirstLine or Diagonal | If the palette has actually 2 dimensions, that is to say it contains 2 or more lines, but the object texture has only one dimenstion, this option is the way of extracting information form this palette.
FirstLine : Keep only the first line of the 2D palette. Diagonal : Take values along the diagonal of the 2D palette. |
| Mixing factor | Enables to change linear combination between the two palettes if you choosed the linear fusion mode. |
When using this menu, Anatomist tries to set an appropriate palette to the object according to its content and to the other loaded objects. For example, Anatomist will choose a one-color palette for a binary image, and a palette with colors distinct from other objects palettes to enable easy combinations of objects.
This menu enables to display the object's palette near the window which contains it. When clicking again on the menu, the palette is hidden.
The palette menu only permits to select an already defined palette and to change its bounds. This new menu enables to create your own palette. The gradient palette edition window show the palette as gradients on RGB + opacity channels. For each channel, you can change the curve. By default each channel function is linear and the result is a gray gradation palette.
It is possible to save the palettes created with this tools. If you save the palette as described here, the palette will appear in Anatomist's list of palettes the next time you will start it.
This menu applies to mesh part of objects. Choose Color => Material in Objet-specific menu or by right-clicking on the object.
Table 5.3. Material
| Option | Description |
|---|---|
Quick selection | Adjustment of the color (or light) and opacity in each point of the mesh . |
Advanced adjustments : Ambient | Ambient light adjustment. |
Advanced adjustments : Diffuse | Same as Quick selection panel. |
Advanced adjustments : Emission | Adjustment of the light emitted by the object. |
Advanced adjustments : Specular | Adjustment of the reflection light seen in front of the object. |
Advanced adjustments : Reflection extent | Inverse of the reflection extent. If the cursor is set to the maximum, it shows a "plastic" effect, otherwise if the cursor is set to the minimum, it appears more "metallic". |
Advanced adjustments : Update mode | Enable/disable automatic update. |
This menu applies to the texture part of objects. Choose Color => Texturing in Object-specific menu or by right-click on the object.
Table 5.4. Mapping Mode
| Option | Description |
|---|---|
|
Geometric |
RGB channels multiplication (between texture and mesh). White color is the 'neutral element'. |
|
Linear |
RGB channels addition weighted by a coefficient. |
|
Replacment |
Only the texture is used and it replaces the mesh color (or previous texture when there are multiple textures). |
|
Decal |
|
|
Blend | |
|
Add |
RGB channels addition. |
|
Combine |
Table 5.5. Texture generation (rarely used option - this generates new texture coordinates on-the-fly)
| Option | Description |
|---|---|
|
None |
No texture generation applied. |
|
Linear-object |
The texture is fixed in relation to the object. |
|
Linerar-eye |
The texture is fixed in relation to observer's eye. |
|
Sphere reflection |
The texture is reflected around the object. |
|
Reflection |
The texture is side reflected. |
|
Normal |
The texture is reflected in relation to the object's normal. |