Welcome to SPIERSedit’s User Manual

[S]erial [P]alaeontological [I]mage [E]diting and [R]endering [S]ystem: Specimen Interpretation and Editing Tool

Main Coding: Mark D. Sutton

Additional Coding: Russell J. Garwood, Alan R.T. Spencer

Documentation: Mark D. Sutton, Russell J. Garwood, Alan R.T. Spencer

SPIERSedit is a package for editing (i.e. preparing) tomographic (slice-based) datasets from any source, for example serial grinding, serial sectioning, or computed tomography, and exporting them as three-dimensional models.

t:@palaeoware

w:https://github.com/palaeoware.

Relevant references

Sutton, M.D., Garwood, R.J., Siveter, D.J. & Siveter, D.J. 2012. Spiers and VAXML; A software toolkit for tomographic visualisation, and a format for virtual specimen interchange. Palaeontologia Electronica 15(2): 15.2.5T

Table of Contents

• 1. Introduction
• 2. Requirements
  • 2.1. System Requirements
  • 2.2. Data requirements
• 3. Basic Concepts
  • 3.1. How SPIERSedit Stores Data
  • 3.2. Downsampling
  • 3.3. Creating a New Dataset
  • 3.4. Window Layout, Zoom, and Navigation
  • 3.5. Threshold image and Linear Generation
  • 3.6. ‘Correct’ Generation
  • 3.7. Generating Multiple Slices
  • 3.8. Editing Requirements
  • 3.9. Simple Editing
  • 3.10. Simple Output (Rendering)
  • 3.11. Saving and Opening Datasets
  • 3.12. Advancing Beyond Basic Concepts
• 4. Masks
  • 4.1. Concepts
  • 4.2. Applying masks
  • 4.3. Advice on use of masks
  • 4.4. Masks manipulation
  • 4.5. Copying Masks
  • 4.6. Masks and Segments
  • 4.7. Masks and Curves
• 5. Segments
  • 5.1. Concepts
  • 5.2. Working with segments
  • 5.3. Advice on use of Segments
  • 5.4. Segment Manipulation
• 6. Range Generation
  • 6.1. Concept
  • 6.2. Range Generation Panel
  • 6.3. Hard and Soft Fills
• 7. Polynomial Generation
  • 7.1. Concepts
  • 7.2. Creating a Sample
  • 7.3. Poly Tab Controls
  • 7.4. Advice on polynomials
• 8. Radial Artefact Correction
  • 8.1. Concept
• 9. Output
  • 9.1. Concepts
  • 9.2. Settings Tab
  • 9.3. Objects Tab
  • 9.4. Output Commands
  • 9.5. Deskewing
• 10. Measuring volumes
• 11. Exporting Working Images
• 12. 3D Brush
• 13. Curves
  • 13.1. Concepts
  • 13.2. Curves Panel
  • 13.3. Editing Curves
  • 13.4. Copying curves
  • 13.5. Interpolating Curves
  • 13.6. Creating Masks from Curves
• 14. Lock/Selection Mode
• 15. Slice Spacing
• 16. Histogram
• 17. Info
• 18. Dataset Downsampling
  • 18.1. Concept
  • 18.2. Changing dataset downsampling
  • 18.3. Dataset downsampling for rough masking
• 19. Advanced Prefs
• 20. Update System