Creating Models of Coral Using Structure from Motion o Presented by Joey Tatroo Supervised by Jules Jaffe

Overviewo Learned coral ecologists interested in calculating

coral surface areao Read Structure from Motion was accurate in-situ

method for calculating surface areao Implemented SfM techniques on a microscopic levelo Generated mesh and model of coralo Deciding direction of research to be done with

meshes

Value of Coralo Forms coral reefs, an extremely diverse ecosystem

• occupies < 0.1% ocean surface• supports > 25% of all marine species• slows currents and breaks waves for coast

o Increases tourism and boosts local economies

Importance of Surface Area and Volumeo Coral has symbiotic relationship with zooxanthellae

• zooxanthellae provides coral with 90% of its energy needs• coral provides zooxanthellae with CO2 needed for photosynthesis• coral provides zooxanthellae with sunlight access

o Zooxanthellae grows in coral tissue• surface area has relationship with coral growth• surface complexity has morphological use

Current Methods for Measurements o In-Situ Methods

• planar projection photography• geometric estimations• stereophotogrammetry

o Lab Methods• in-situ methods• wax coating• computer tomography

Comparison of Techniques

o Structure from motion found to be within 8% of CT• Paper used 10 Megapixel camera with field of view of 20cm x 20cm• http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12331/full

o Motivated desire to examine corals on microscopic level

Basics of Creating SfM Model

Structure from

Motion

Multi View Stereo

Model Fitting

Texture Mapping

Setup in the Optics Lab o Used prototype Keck microscope to collect images

• pixel size < 3.63 microns (conservative estimate)

• field of view < 7.43 mm2

• depth scanning microscope

o Used pyramid stacking methods in Helicon Focuso Used Agisoft to create 3D mesh of coral

Focal Stacking the Imageso Captured 40 slices of an imageo Determined which of the images were in focuso Used pyramid method for focal stacking

Some of the Images Collected

Some of the Focal Stacked Images

Running the Images through Agisofto Imaged the coral from two different vertical angleso Rotated the coral 5 degrees horizontally per angle

SfM Pipeline in PicturesAlignment

Point Cloud

Dense Point Cloud

3D Mesh

Textured Model

Here’s a 3D Printed Coral!o Using lab’s 3D Printer, a model was createdo Cool right?o Give it 30 yearso Point Cloud

What’s Next?o Setting up additional processor to quickly create mesheso Determining software program to analyze morphology

(ArcGIS possibly)o Choosing direction of research

• Finding how surface complexity scales with resolution• Looking at evolutionary morphology using conformal geometry• Comparing metrics across methods to compute surface area

o Special thanks to Jules Jaffe, Paul Roberts, and Ben Laxton