Interacting with Amira
When you initially open amira, 3 windows (either separate or conjoined will pop up). The 3 windows include a Viewer Window, a Console Window, and a main window. Each will be explained below. If the windows are conjoined, you can separate them following instructions on Viewer Options in Amira
The Viewer Window
The viewer window is primarily responsible for showing you the data with which you want to interact with. In Segmentation mode, it shows slice data and a 3D viewer of your model in progress. In Pool mode, the viewer show your model with intact surfaces.
Buttons atop the viewer window are white, black and blue and allow you to interact with the data on the screen. For more information on the function of these buttons visit Amira Interface: 3D and Slice Data Sets
The Console Window
The console window shows you what Amira is currently processing. While working in amira, you will not have to interact with this window and may close it. It is useful however for showing you what problems are with processing data, and where the error occurs. For instance if you attempt to open a file, it will list a series of events carried out by amira to open your file. It will also show if they are successful or not and acts as a good trouble shooting area should problems arise.
The Main Window
The main window is the one used for majorly interacting with your model, slice data and Amira in General. It is here where you will select how you will interact with Amira, mainly what mode you wish to work in -- Segmentation or Pool view.
Upon opening Amira the Main window will be entitled "Amira - Your File Name"
To enter segmentation mode, click the segmentation button (top of screen, looks like 3 stacked slices, 4th from left) in the Main window.
Within Segmentation mode, the Main Window will house:
- Segmentation Tools
- The Materials Window
- Selection tools (add and delete materials)
- Display and masking tools (to interact with the 3D portion of the slice viewer)
In Segmentation mode, you interact with 2D slice data (in your Viewer Window) to segment out your materials and begin building your surfaces.
For a greater description of how to segment your materials visit Segmentation in Amira
To enter pool mode, click on the pool button (top of screen, looks like 3 bubbles joined by lines, 1st from left) in the Main window
Within the pool mode, you will be able to generate surfaces for the materials you create in segmentation mode. This is where you piece together an interactive model. You may also choose to smooth surfaces, create videos and export surface files.
In this window there are 2 separate areas. Within the "Pool" area you will see various bubbles representing your segmented data which ultimately make up your model. Within the "Properties" area, you will see details on each bubbled piece of information in the pool area, and be able to better refine what is displayed.