Agenda

Course Contents

• First steps in Amira
  • 1.1 Getting started
  • 1.1.1 Exercise: Getting started
  • 1.2 Some concepts of the graphical user interface
  • 1.2.1 The Pool area
  • 1.2.2 The Properties area
  • 1.2.3 Exercise: Becoming familiar with the graphical user interface (GUI)
  • 1.3 The 3D Viewer
  • 1.3.1 Multiple viewer layouts
  • 1.3.2 Exercise: The 3D Viewer
  • 1.3.3 Quick reference to the viewer toolbar
  • 1.4 How to load image data
  • 1.4.1 Setting the le format
  • 1.4.2 Reading 3D image data from multiple 2D slices
  • 1.4.3 Setting the bounding box
  • 1.4.4 The Stacked Slices le format
  • 1.4.5 Exercise: Loading 3D images
• 2 Visualization of 3D images
  • 2.1 Orthogonal and oblique slicing
  • 2.1.1 Exercise: Visualization } slicing
  • 2.2 Isosurface
  • 2.2.1 Exercise: Visualization } isosurface
  • 2.3 Volume Rendering
  • 2.4 Cropping a visualization: SelectRoi
  • 2.4.1 Exercise: Visualization } volume rendering
• 3 Image segmentation and surface reconstruction
  • 3.1 Working with the Segmentation Editor
  • 3.1.1 Customizing the display:
  • 3.1.2 The Selection toolbar
  • 3.1.3 The Display and Masking toolbar
  • 3.1.4 Quick reference to the most important segmentation tools
  • 3.1.5 Further tools available in the Selection menu of the Segmentation Editor
  • 3.1.6 Exercise: Segmentation
  • 3.2 Surface generation from segmentation results
  • 3.3 Simplifying and smoothing surfaces
  • 3.3.1 The Surface Simplication Editor
  • 3.3.2 Smoothing surfaces
  • 3.4 Visualizing surfaces with SurfaceView
  • 3.4.1 Exercise: Generate a surface model from your segmentation, smooth, and visualize the surface
• 4 Measuring and manipulating images
  • 4.1 Measuring volume, area, and length
  • 4.1.1 MaterialStatistics
  • 4.1.2 SurfaceArea
  • 4.1.3 LineProbe
  • 4.1.4 Measurement
  • 4.1.5 Exercise: Basic measurement
  • (c) 2003, 2009, 2012 Visualization Sciences Group, Inc. 2 amira(r) Illustrated Tutorial
  • 4.2 Transformations, Transform Editor
  • 4.2.1 The Transformer manipulator
  • 4.2.2 Exercise: Transformations, Transform Editor
  • 4.3 Resampling, cropping, changing data type
  • 4.3.1 Resampling
  • 4.3.2 Cropping data
  • 4.3.3 Converting to monochrome data
  • 4.3.4 Converting stacked to uniform coordinates
  • 4.3.5 Exercise: Resampling, cropping, changing data type
• 5 Working with large data 46 5.1 Memory limitations in 32-bit environments
  • 5.2 The LDA format
  • 5.2.1 Exercise: Working with large data: LDA, ExternalDiskData