Visualizing your Amira Model
For more information on pool mode visit Interacting with Amira
If you have just opened Amira for the first time, the main and viewer windows are already formatted to be in pool mode. To get started you will need to upload a data set to the file on which to work. To do this please view instructions at Uploading Data into Amira.
If you are attempting to load a previously created network: Click File > Open Network. This will open a Load Network Window. Find your desired file and Click Load Opening an existing network will populate the main window with bubbles of information which you previously created. You can use these bubbles to modify your 3D surfaces which will be explained below.
Visualizing your Model
In order to visualize your model, you will need to be in Pool Mode. To do this, click the pool button (below file) on the main window.
Creating a Master Surface
In order to see a smoothed 3D version of your model you will need to generate a series of surfaces to wrap around the materials you originally created in segmentation mode. To do this:
1. Right click your labels file (a green bubble located under your original data bubble) to open a drop down menu
2. Choose Compute > SurfaceGen. This will cause a red bubble to pop up which will be joined to your labels file via a line segment.
3. Click on the red SurfaceGen bubble. In the bottom half of the pool window, click apply. This process will take some time, depending on the size of your model. You will see a red bar process across the bottom of the screen showing Amira's progress in processing this action.
Note: When creating a SurfaceGen, you are able to change the degree of smoothing initially applied to each surface. This is particularly important as smoothing may cause some small or thin structures to not appear at all. There are three options available for the initial smoothing pass: none, constrained smoothing and unconstrained smoothing. This drop down box is located in the properties portion of the main window next to smoothing:. Each option does as follows:
- None: no smoothing is applied when the surface is created. This will cause each surface to appear as a block rendering (showing the specific voxels you originally segmented), and will not be smooth, preserving the highest level of detail that you segmented originally. . This will also take the longest amount of time to complete. Choose this option if you want to create surfaces of very small objects or objects with thin portions to prevent pieces from not appearing.
- Constrained Smoothing: Will create a smoothed surface under certain constraints meaning that there is a limited amount of edge blending which may be carried out by the program based on the segmentation pattern of the structure. This is an option between the "none" and "unconstrained smoothing" options.
- Unconstrained Smoothing: Creates a smoothed surface with few constraints, meaning you get a smoother representation, with a loss in detail.
Bear in mind that individual surfaces(see below) may be created in any of the above smoothing options) and can be further smoothed individually. This means that if you have a couple of small or thin surfaces, and other large surfaces, you can apply different options to each surface. Do this by rendering a master surface with "none" as your smoothing option first and creating your small individual surfaces. Then re-generate your master surface using constrained or unconstrained smoothing to create your larger individual surfaces.
To re-generate your master surface, click on your red surfacegen bubble, select a smoothing option from the drop down box, and click apply. You can now interact with your master surfaces created in your new smoothing parameter.
4. Upon this action completing, a new green labels bubble will pop up joined to the red SurfaceGen bubble.
5. Right click the new labels bubble and select Display > SurfaceView. This will cause a yellow SurfaceView bubble to pop up joined to the labels file. You should now be able to visualize your entire model in a smoothed form in the Amira viewer window. Click the small box within SurfaceView bubble to toggle the model on and off. (orange = on, grey = off)
The above instructions just created a master surface file containing all of the individual surfaces included in your model. Toggling this file will turn all included surfaces on and off at once. To separate these surfaces into individual files which are able to be controlled independently of eachother, you must create individual surfaces
Creating Individual Surfaces
To create an individual surface, you must first create a master surface which will be linked to your SurfaceGen and Labels files. Follow the above instructions to get to this point.
To create a new surface file for an individual material:
1. Click on your Master surface file (yellow bubble). Make sure that the toggle box is on by clicking it until it turns orange.
2. Within the properties section of pool mode, click the drop down box adjacent to Materials. Sellect All. This will cause your entire model to become highlighted in red in the Amira Viewer window.
3. Click the Remove button next to the Buffer title in the properties window of pool mode. Your viewer window should now be blank.
4. Re-click on the drop down box adjacent to the Materials title. Select the material you want to create a surface for. That individual material should now appear as a red colour in the viewer box. It will also have a black cube with lime green corners around it. This is the bounding box and represents the space in which your entire data set exists.
5. Click the add button within the rpoperties section (next to remove). This will change the colour of the material you selected to match the original colour you segmented it in. This colour can be changed later as explained below.
6. If you wish to add multiple materials to this surface file, repeat steps 4 and 5 again adding as many materials as you wish, then proceed to step 7. If you do not want to add any more materials to this file, proceed to step 7.
7. Click the more options drop down box within the properties section and choose Create Surface. A green label file will pop up somewhere on the screen which isn't connected to any other bubble. This is your new label file for the materials you selected in steps 4-6.
8. Toggle your master surface to off by clicking the small orange box within the surfaceView bubble until it is grey. Your viewer window should now be blank.
9. Click on your new label file and drag it to wherever you want on the screen. You now need to add a surface file to visualize the label. To do so, right click on the label file to open a drop down menu. Choose Display > SurfaceView. There may also be a yellow button acting as a shortcut below the original open data button at the top of your main window. This will perform the same function. This will cause a yellow surface bubble to pop up adjoined to the green label file. Your surface should now also be visualized within the viewer window.
10. Your surface may appear to have holes in it in places where it was touching other materials. This is a minor bug which can be easily fixed. (see below)
Duplicating a Surface
to duplicate a surface file (yellow bubble)
1. Right mouse click the yellow surface file you want to duplicate to open a drop down menu
2. Select Duplicate A new surface file will appear attached to the original green label file.
Fixing holes in Surfaces
To solidfy your surface, clik on the surface view file you wish to correct. Within the properties section, click the drop down box adjacent to "Materials" and again select your desired surface from the list. This will highlight the surface in red within the viewer window. Click Add. Your surface should now be free of holes.
Changing the colour of a surface
To change the colour of a surface: 1. Click the yellow surface bubble of the surface you wish to change the colour of.
2. Within the properties section, click the drop down box next to Colours and choose Constant. This will change the surface to a red colour, and will add a colourmap section to the properties area.
3. Double click the red checkered box next to colourmap to open a colour wheel. Use the 4 slide bars or click the shaded box to alter the colour as you wish. Once finished, click apply.
Changing the drawing style of a surface
To change the transparancy or drawing style ofa surface: 1. click the yellow surface bubble of the surface you wish to alter
2. within the properties section, click the drop down box next to Draw Style and make your selection. You can choose from:
- Shaded = Solid, opaque shell
- Outlined = Solid, opaque shell overlayed with lines denoting the edges of the polygon faces making up your surface
- Lines = Shape is made up of the same lines displayed in "outlined" showing the edges of polygon faces making up your surface. Additional colours shown in these lines denote areas of contact with other shapes
- Points = Shows your surface as dots where polygon corners meet (intersections out "outlined" lines)
- Transparent = Shows a transparent rendering of your surface. You can alter the degree of transparency by using the slide bar within the properties section next to Base trans. A cautionary note is that when applied to large structures with a lot of detail, transparency really slows the computer down.
Note: If you want to create a movie that shows your surface in multiple drawing styles (ie. shaded and transparent) you can create duplicate surfaces of the same material and apply different drawing styles to each surface file. Then in your movie you can simply refer to individual surface files separately to change the drawing style displayed.
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