3DK Knowledge Project


Overview
Research Team
Pilot Projects
Feature Extraction and Analysis
Data Flow in the 3D Knowledge System
Visual Query Interface
Evaluation and Assessment

Pilot Projects

 

The pilot projects include shape characterization of archaeological artifacts (BONES, VESSELS, LITHICS); shapes and forms of intracellular bio-molecular machines to gain insight into their functions (CELLS, BIO-STRUCTURES) and spatial symmetry in phenomena observed in experimental simulations in Plant Biology (DIATOMS).

Bone

Bone Joint Classification: The goal is to learn about the ability of fossil human ancestors to walk upright and make tools by developing biomechanical models of locomotion and manipulative movements with 3D osteological data. Use of calipers and visual inspection is inadequate to capture the complex curvatures of 3D joint surfaces.

Cells

Molecular & Cell Biology: The mechanisms regulating life itself remain difficult to address without understanding the shape, form, function, and regulation of the bio-molecular machines in a cell. Traditional methods are inadequate in identifying the shape and the quantification of the structures in a cell.

Vessel

Ceramic Vessel Classification: The goal is to learn about vessel uniformity and proportionality for different functions as indicators of developing craft specialization and complex social organization among prehistoric cultures. Use of metric rulers and visual inspection are inadequate to accurately capture the complex curvatures and proportionality of vessel forms and sizes.

Ultrasound

Ultrasound Data Modeling ( UCSD): The project aims to readily recognize features in 3D ultrasound volume data sets and distinguish between real and spurious artifacts. Features in new data sets cannot currently be compared due to lack of adequate feature recognition and indexing procedures.

Lithic

Lithic Refitting: The project goal is reconstruction of stone tool manufacturing activities within prehistoric archaeological sites. Refitting lithic artifacts by manual trial and error is an accurate but labor intensive method. Automated 3D surface matching of conjoinable artifacts will enhance the efficiency of this valuable analytic method.

Diatom

Diatom Classification: The project aims to understand pattern morphogenesis of diatoms which display a seemingly endless variety of 3D structures and architectures from essentially amorphous silica glass. The extremely large domain of over 50,000 species, with subtle variations in each, and data from several diverse techniques makes identification tedious and difficult even for the expert.





Bone Joint Classification


3D Topography of Joint Surfaces (Surface Data): Paleoanthropology
The goal is to learn about the ability of fossil human ancestors to walk upright and make tools by developing biomechanical models of locomotion and manipulative movements with 3D osteological data. Use of calipers and visual inspection is inadequate to capture the complex curvatures of 3D joint surfaces.

Research Team: Marzke, Razdan, Henderson, Farin, and Panchanathan

Problem: To learn about the ability of fossil human ancestors to walk upright and make tools by developing biomechanical models of locomotor and manipulative movements with 3D osteological data.

Current Limitations: Use of calipers and visual inspection are inadequate to capture the complex curvatures of 3D joint surfaces and control for body size differences in cross-species comparisons.

Expected Breakthrough:Capture 3D data on bones and do scalable, visual, and quantitative comparisons of relative and reciprocal joint surface areas and curvatures of living and fossil apes and human.

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Molecular & Cell Biology


Choreography of Cellular Events (Volume Data) (Phase I): Molecular & Cell Biology
The mechanisms regulating life itself remain difficult to address without understanding the shape, form, function, and regulation of the bio-molecular machines in a cell. Traditional methods are inadequate in identifying the shape and the quantification of the structures in a cell.

Research Team: Capco, Farin, Panchanathan, Nielson, Bailey, and Razdan

Problem: The mechanisms regulating life itself remain difficult to address without understanding the shape, form, function, and regulation of the bio-molecular machines in a cell.

Current Limitations: Traditional methods of viewing sliced images of cells are inadequate in identifying the shape and the quantification of the structures in a cell.

Expected Breakthrough: Correlating the shapes of bio-molecular machines with their functions will enable the understanding of post-fertilization choreography of the cellular events which in part will provide crucial answers for research in cloning of agricultural animals.

2D image slices from LSCM 2D image slices from LSCM 2D image slices from LSCM

2D image slices from LSCM describing the volume inside the cell are used to construct a 3D volumetric mathematical model: the filtered image shows the DNA as a donut shaped artifact.

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Ceramic Vessel Classification


3D Morphology of Ceramic Vessels (Surface Data) (Phase I): Archaeology
The goal is to learn about vessel uniformity and proportionality for different functions as indicators of developing craft specialization and complex social organization among prehistoric cultures. Use of metric rulers and visual inspection are inadequate to accurately capture the complex curvatures and proportionality of vessel forms and sizes.

Research Team: Simon, Razdan, Farin, Collins, Panchanathan, and Henderson

Problem: To learn about vessel uniformity and proportionality for different functions as indicators of developing craft specialization and complex social organization among prehistoric cultures.

Current Limitations: Use of metric rulers and visual inspection (2D profiles) are inadequate to accurately capture the complex curvatures and proportionality of vessel forms and sizes.

Expected Breakthrough:Capture 3D data from vessels for scalable, visual, and quantitative comparisons of curvatures, volumetrics, and proportionality for study of prehistoric pottery traditions.

Views from the 3D interface
Views from the 3D interface
Views from the 3D interface
Views from the 3D interface
Views from the 3D interface

Views from the 3D interface developed for feature identification and profile graphing of prehistoric ceramic vessels: examples [SIMO97, SIMO98] illustrating complex curvatures and detailed subfeatures on snake and horned toad effigy jars scheduled for reburial by Native Americans in June, 1999.

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Ultrasound Data Modeling ( UCSD)


Biological Structure Recognition (Volume Data) (Phase II):
Bio-Technology @ UCSD

The project aims to readily recognize features in 3D ultrasound volume data sets and distinguish between real and spurious artifacts. Features in new data sets cannot currently be compared due to lack of adequate feature recognition and indexing procedures. Research Team: Bailey, Nielson, Razdan, Henderson, Farin, and PanchanathanProblem: To readily recognize features in 3D ultrasound volume data sets and distinguish between real and spurious artifacts.Current Limitations: Features in new data sets cannot currently be compared due to lack of adequate feature recognition and indexing procedures.Expected Breakthrough:Archive 3D ultrasound data in a meaningful multiresolution way and develop fast, interactive graphics tools that will allow the user to visually inspect the target and the matched volume simultaneously.

3D Volume Dataset aquired from Ultrasound and physically prototyped output.
3D Volume Dataset aquired from Ultrasound and physically prototyped output.
 

3D Volume Dataset aquired from Ultrasound and physically prototyped output.


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Lithic Refitting


Lithic Tool Manufacturing and Refitting (Surface Data) (Phase II): Archaeology
The project goal is reconstruction of stone tool manufacturing activities within prehistoric archaeological sites. Refitting lithic artifacts by manual trial and error is an accurate but labor intensive method. Automated 3D surface matching of conjoinable artifacts will enhance the efficiency of this valuable analytic method.

Research Team: McCartney, Razdan, Henderson, Farin, and Panchanathan

Problem: Reconstruction of stone tool manufacturing activities within prehistoric archaeological sites and related cultural behaviors require identifying sequences of conjoining lithic artifacts.

Current Limitations: Refitting lithic artifacts by manual trial and error is an accurate, but highly labor-intensive, method thatrequires the entire sample of artifacts to be present in a single lab, conditions not always possible given various antiquities restrictions.

Expected Breakthrough: Automated 3D surface matching of conjoinable artifacts will dramatically enhance the efficiency of this valuable analytic method and extend the scope of searches to collections from different sites without requiring transport of the actual materials.

Conjoining flake scars on core and flake surfaces.

Conjoining flake scars on core and flake surfaces. Flakes are successively separated from the core resulting in matching flake

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Diatom Classification


3D Structures of Diatoms (Surface and Volume Data) (Phase II): Plant Biology
The project aims to understand pattern morphogenesis of diatoms which display a seemingly endless variety of 3D structures and architectures from essentially amorphous silica glass. The extremely large domain of over 50,000 species, with subtle variations in each, and data from several diverse techniques makes identification tedious and difficult even for the expert.

Research Team: Ramakrishna, Razdan, Henderson, Farin, Panchanathan, and Bailey

Problem: To understand pattern morphogenesis of diatoms which display a seemingly endless variety of 3D structures and architectures from essentially amorphous silica glass

Current Limitations: The extremely large domain of over 50,000 species, with subtle variations in each, and data from several diverse techniques makes identification tedious and difficult even for the expert. Effective quantitative methods for analysis of structure, modeling, and automatic computerized algorithms for fast feedback are lacking

Expected Breakthrough: Creation and sharing of 3D data sets, pattern recognition tools, and analysis software on diatoms for scalable, visual, and quantitative comparisons of surfaces, curvatures, and internal structure for classification and nanotechnology applications.

Examples of complex 3D architectures and subtle subfeatures of micron-sized diatoms exhibiting different planes of symmetry and pore structure.



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