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Reconstruct - User's Manual

CHAPTER 1 Quick Start
- Create a Series
- Import Section Images
- Calibrate Pixel Size
- Align Sections
- Trace Profiles
- View Three-Dimensional Object
- About the Rest of the Book
CHAPTER 2 (TBD)
CHAPTER 3 Software Overview
- Series, Sections, Domains, Traces, and Objects
- Data File Organization
  - XML File Formats
- System Requirements
  - Operating System
  - OpenGL
  - Hardware Requirements
- History
- Credits
  - Source Code
  - Development Tools
CHAPTER 4 User Interface
- Windows and Dialogs
  - Resizing and Moving Windows
  - Switching Between Windows
- Main Window
- Main Menu
- Tools Window
- Status Bar
- Section List Window
- Thumbnails Window
- Domain List Window
- Trace List Window
- Trace Palette Window
- Object List Window
- 3D Scene Window
- Z-Trace List Window
- Distance List Window
- Exiting or Aborting
CHAPTER 5 Series
- Creating a Series
- Opening and Closing Series
- Saving a Series
- Series Options
- Exporting and Importing Images
- Exporting Trace Lists
- Importing Series Data
CHAPTER 6 Sections
- Section Indexing
- Creating a Section
- Saving a Section
- Displaying a Section
  - Centering
  - Zooming and Panning
- Paging Sections
- Blending and Flickering Sections
- Listing all Sections
- Editing Section Attributes
  - Movement Lock
  - Thickness
  - Section Numbering
- Deleting Sections
- The UNDO Stack
- Thumbnails
- Exporting Section Images
CHAPTER 7 Domains
- Creating a Domain
- Listing Domains
- Selecting a Domain
- Merging a Domain
- Domain Attributes
  - Name
  - Source
  - Pixel Size
  - Contrast and Brightness
- Domain Boundary
- Hiding Domains
- Proxies
- Proxy Rule of Thumb for Single Domains
CHAPTER 8 Traces
- Creating a Trace
  - Ellipse Tool
  - Line Tool
  - Rectangle Tool
- Selecting Traces
  - Selection Tool
  - Deselecting Traces
  - Zooming to Selected Traces
- Trace List
- About Trace Names
- Trace Attributes
  - Name
  - Comment
  - Hidden
  - Simplified
  - Closed
  - Border Color
  - Fill Color
  - Fill Style
- Trace Clipboard
- Setting Trace Attributes for Drawing
- The Trace Palette
- Stamping Predefined Shapes
- Creating a Grid of Traces
- Open Point-by-Point Drawing
- Closed Point-by-Point Drawing
- Freehand Drawing
- Editing Traces
  - Merge
  - Reverse
  - Simplify
- Wildfire Region Growing
- Z-Traces
CHAPTER 9 Calibration and Measurement
- Units of Measurement
  - Data Precision
  - Image Pixel Size
- Cal Grids and Scale Bars
- Calibrating Traces
  - Drawing Calibration Traces
  - Calibrate Selected Traces
  - Resize Traces, Set Pixel Size, or Scale Section
  - Apply the Calibration to Other Sections
- Section Thickness
  - Calibrating Section Thickness
- Z Distance
- Status Bar Measurements
- Domain List Measurements
  - Length
  - Area
  - Midpoint X
  - Midpoint Y
- Trace List Measurements
  - Length
  - Area
  - Centroid X
  - Centroid Y
  - Min X
  - Min Y
  - Max X
  - Max Y
  - Z Position
  - Thickness
- Object List Measurements
  - Count
  - Surface Area
  - Flat Area
  - Volume
- Z-Trace List Measurements
  - Length
- Distances List Computation
  - Algorithm
CHAPTER 10 Movements and Alignments
- Transformations
- Keyboard Increments
- Movement Type-In Dialog
- Undoing Movements
- Repeating Movements
  - Propagate
  - Repeating Movement Sequences
- Alignments
  - Aligning Selected Traces
  - Aligning Entire Sections
- Evaluating Alignments
- Undoing and Adjusting Alignments
- Repeating an Alignment
- Montaging Domains by Point Correspondences
- Aligning By Correlation
- Tips for Aligning Sections
  - One Strategy
CHAPTER 11 Objects
- The Object List
- Changing Object Attributes
- Simplifying Objects
- Deleting Objects
- 3D Object Representations
  - Traces
  - Trace Areas
  - Trace Midpoints
  - Box
  - Boissonnat Surface
  - Cylinder
  - Ellipsoid
  - Sphere
  - 3D Parameters
    - Shift Object By
    - Surface Normals
    - Faceting Density
    - Size
    - Boissonnat Surfaces
- Z-Trace List
CHAPTER 12 The 3D Scene
- OpenGL Rendering
- Composing a Scene
  - Adding Objects
  - Removing Objects
  - Changing Object Appearance
    - Diffuse Color
    - Emissive Color
    - Ambient Intensity
    - Transparency
    - Specular Color
    - Shininess
    - Filled or Wireframe Faces
- Viewing a Scene
  - Rotating, Panning, and Zooming
  - Spin
  - Background Color
- Saving a Scene
  - VRML 2.0
  - Bitmap Image
  - VRML 1.0
  - DXF
CHAPTER 13 (TBD)
Bibliography
Appendices
- Keyboard Overlay