David F. Wiley, Nina Amenta, Dan A. Alcantara, Deboshmita Ghosh, Yong J Kil, Eric Delson, Will Harcourt-Smith, F. James Rohlf, Katherine St. John, Bernd Hamann, Ryosuke Motani, Steven Frost, Alfred L. Rosenberger, Lissa Tallman, Todd Disotell, and Rob O'Neill
We propose to develop software tools for the analysis, interpretation and visualization of three-dimensional shape data from living and extinct organisms, using the statistical framework of geometric morphometics. While this software will be widely useful in biology and paleontology, we plan to focus our work by concentrating on one significant problem: incorporating fossils into evolutionary trees. Evolutionary trees for groups of living species are usually estimated using DNA sequence data. Since this is usually not available for extinct species, we need to use morphology (the shapes of fossil and modern specimens) to decide how the extinct species should be included in a tree whose framework is based on molecular studies. Specifically, we plan to estimate a well-supported evolutionary tree for the mainly African papionin monkeys, an inherently interesting group that includes about as many extinct as living clusters of species. Our analysis will be based on a large existing database of three-dimensional data (mostly skull surfaces) at the American Museum of Natural History.
This end-to-end analysis project should produce research results at all levels. The interactive graphics, visualization and statistical analysis tools we propose are ever more widely needed as the amount of three-dimensional morphology data increases. We expect that the close interaction of geometric morphometrics and computer graphics will lead to new ideas about the representation of shape. We have new approaches to the problem of integrating morphology with molecular data in the study of evolution, which we hope will be successful and applicable in many parts of the tree of life. And with massive amounts of new data, new processing and analytic software, and new approaches to integrating morphology, we hope to be able to answer specific questions about the evolution of African monkeys, which have remained elusive up until now.
Our proposed work will have a variety of broader impacts beyond our own research agendas. A large part of the project will be done at Lehman College of CUNY, a minority-serving institution in the Bronx, and minority undergraduates are already involved in the research. The software tools we will develop are sorely needed and will become part of the scientific infrastructure and our visualizations will form a basis for sharing research in evolution with the general public.
AAAS/NSF Scientific Visualization Competition Entry
Below is our five-minute video submission into the non-interactive media category for which we won an honorable mention award.
Our press release.
IEEE Visualization 2005
Download the powerpoint presentation given at Vis (ZIP 53MB)
Below is our five-minute video submission that accompanies our Visualization 2005 paper. This video is a bit more technical than our NSF video above.
Landmark was developed by the scientists at the Institute for Data Analysis and Visualization (IDAV) and the University of California, Davis. Working together with collaborators at the American Museum of Natural History, the team was able to build an easy to use tool for landmark editing and placement on geometric surfaces typically obtained via laser range scans.
The main purpose of Landmark is to easily place landmark points and semi-landmark points accurately and with high repeatability on complex surfaces for the purpose of registration, alignment, morphing, and computation of hypothetical ancestors in evolutionary trees.Features include:
- Point, curve, and patch primitives for placing the exact type of landmark point you're interested in
- Exporting of landmark points for use in other applications
- Correspondence between landmark points on different surfaces
- Automatic inference of landmark correspondences based upon existing relationships
- Semi-automatic transference of landmark points from one surface to another
- Built-in morphing between two surfaces
- Transparent surface rendering allowing interior inspection of surfaces
- Easy to use 3D interface for manipulating surfaces and landmark primitives
- Retrodeformation for un-deforming fossils
- Two-dimensional warping and merging
- Importing landmark points into Landmark
- File management for large projects
- A plugin interface
- Measurement calibration
- Reorder landmark primitives easily
- Transverse/coronal plane specification
- Improved landmark manipulation
- Handles missing data
Coming soon...We are currently working on:
- Employment of low-resolution models for interactivity
- Improving retrodeformation
- Fixing broken fossils
- Flexible patches
- Mesh coloring based upon curvature
The Landmark documentation is provided in PDF format and demonstrates a tutorial for two crania surfaces. It can be downloaded seperately by the following link (it is included in the software distribution below):Download Here (PDF 12.8MB)
Landmark is currently only available for Microsoft Windows. Download a zipped installation from the following link:Download Here (EXE 20MB)
Current release is version 3.6
- November 6, 2007: Fixed PLY reading problem for some PLY models. Added a number of improvements.
- April 4, 2006: Fixed PLY reading problem for some PLY models.
- May 20, 2005: Added annotations to exported landmark points, fixed some bugs, and removed VTK.
- Apr 23, 2005: Added a video and a tree image to the Screenshots section.
- Feb 25, 2005: Fixed point exporting crash and missplaced points.
- Jan 26, 2005: Fixed rendering bug.
- Jan 25, 2005: Fixed the PHANTOMIOLIB42.DLL problem when starting the application.
- David F. Wiley (1,2)
- Nina Amenta (1,2)
- Eric Delson (4,5,6,7,8)
- F. James Rohlf (3,4,5,6)
- Bernd Hamann (1,2)
- Katherine St. John (5,6,9)
- Dan Anthony Alcantara (1,2)
- Yong J. Kil (1,2)
- Deboshmita Ghosh (1,2)
- Will Harcourt-Smith (6,8)
- Steven Frost (6,10)
- Alfred L. Rosenberger (4,5,6,11)
- Lissa Tallman (4,5,6,7)
- Todd Disotell (5,12)
- Rob O'Neill (6,13)
- Institute for Data Analysis and Visualization, University of California, Davis
- Department of Computer Science, University of California, Davis
- Department of Evolution and Ecology, Stony Brook University
- Ph.D. Program in Anthropology, City University of New York
- NYCEP (New York Consortium in Evolutionary Primatology)
- NYCEP Morphometrics Group
- Department of Anthropology, Lehman College/CUNY
- Division of Paleontology, American Museum of Natural History
- Department of Mathematics and Computer Science, Lehman College/CUNY
- Department of Anthropology, University of Oregon
- Department of Anthropology, Brooklyn College, CUNY
- Department of Anthropology, New York University
- Digital Arts Research Laboratory, Pratt Institute
- Ryosuke Motani, Nina Amenta, David F. Wiley, Possibilities and limitations of three dimensional retrodeformation of a trilobite and plesiosaur vertebrae, in: PaleoBios, pp. 88, 2005.
- David F. Wiley, Nina Amenta, Dan A. Alcantara, Deboshmita Ghosh, Yong J Kil, Eric Delson, Will Harcourt-Smith, F. James Rohlf, Katherine St. John, Bernd Hamann, Evolutionary Morphing, in: Proceedings of IEEE Visualization 2005, 2005.
- Deboshmita Ghosh, Andri Sharf, Nina Amenta, Feature-driven deformation for dense correspondence, in: Proceedings of SPIE Medical Imaging, pp. 36, 2009.
- Misha Kazhdan, Nina Amenta, Shengyin Gu, David F. Wiley, Bernd Hamann,
This material is based upon work supported by the National Science Foundation under Grant No. SEI(SBE)-0513894. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.
Preliminary work of this material was supported by the National Science Foundation under Grant Nos. DEB-0121681/0121682, ACI-9982351, DEB-0212023, ACI-962034, and NIH/NSF P20 MH60975-06A2.
Copyright (C) 2002-2006 by David F. Wiley and the Institute of Data Analysis and Visualization (IDAV)