TABLE 1. Ten step workflow for virtual fossil preparation.
|
Task |
Step |
Process |
|
Reconstruct |
1 |
Reduce blurring by applying noise reduction (see method) |
|
2 |
Reduce cupping by applying beam hardening correction (see method) |
|
|
3 |
Increase contrast by stretching floating point range of fossil grey values |
|
|
Render |
4 |
Segment fossil from matrix by applying global threshold (Fig.3A) |
|
5 |
Segment fossil form non-adjacent matrix using region grower tool (Fig. 3B) |
|
|
6 |
Remove adjacent matrix with a masking tool (Fig.3C) |
|
|
7 |
Repeat steps 4-7 to segment anatomical features (Fig. 3D) |
|
|
8 |
Apply lighting and false colour to create virtual specimen see (Fig. 4) |
|
|
9 |
Animate rendered 3D model using a keyframer (Fig. 6) |
|
|
Store |
10 |
Archive slice stack as 8 Bit BMP, 16 Bit DICOM or 32 Bit vol files. |
TABLE 2. Data processing software for voxel and surface based 2D and 3D data. The useful tools and applications included in the packages are highlighted.
|
Package |
Source |
Surface Determination |
Magic Wand |
Masking |
Rendering |
Stereo-Anaglyphs |
Movie Animation |
STL Files |
Traditional Morphometrics |
Geometric Morphometrics |
URL |
|
VG Studio Max |
Commercial |
3D |
3D |
2D |
3D |
3D |
3D |
3D |
3D |
3D |
www.volumegraphics.com |
|
SPIERS |
Freeware |
3D |
|
2D |
3D |
3D |
|
|
|
|
www.spiers-software.org/ |
|
DRISHTI |
Freeware |
|
|
|
3D |
3D |
3D |
|
|
|
www.sf.anu.edu.au/Vizlab/drishti/ |
|
ImageJ |
Open Source |
|
2D |
2D |
3D |
|
|
|
3D |
2D |
www.rsb.info.nih.gov/ij/ |
|
Mimics |
Commercial |
3D |
2D |
3D |
3D |
|
|
3D |
|
|
www.materialise.com/mimics |
|
Simpleware |
Commercial |
2D |
2D |
2D |
3D |
|
3D |
3D |
3D |
|
www.simpleware.com |
|
Amira |
Commercial |
3D |
2D |
2D |
3D |
|
3D |
3D |
|
|
www.amira.com/ |
|
Blender |
Open Source |
|
|
|
3D |
|
3D |
|
|
|
www.blender.org |
|
Stratovan Checkpoint |
Commercial |
|
|
|
|
|
|
|
3D |
3D |
www.stratovan.com |
|
Meshlab |
Commercial |
|
|
|
|
|
|
3D |
|
3D |
www.meshlab.sourceforge.net/ |
|
Simpleware |
Commercial |
2D |
2D |
2D |
3D |
|
3D |
3D |
3D |
|
www.simpleware.com |
