Week 8 - 620

News

This past week the Smithsonian held a conference to talk about and demonstrate their attempts to digitize collection. Their pilot program released a dedicated website to host a series of objects from the institution's collections and a powerful 3D viewer to present them. These objects include prehistoric whale skeletons, CT-scanned insects, even a whole mammoth skeleton. Everything they mentioned echoes what my thesis has been striving for: accessibility, engaging the public, mobilizing the 99% of collections that remain undisplayed, and science outreach. This is only the most recent example of a digital museum collection announcement. 

Website

I set up a quick Wordpress site to eventually host my final animation. Other digital museum objects are being given dedicated sites, so I think this is the way to go. Right now I just a placeholder Vimeo video and a p3d.in embedded 3D model, but eventually there will be more content associated with the project (concept art, etc).

The site is available here:
http://www.danieljoelnewman.com/bothriolepis/

Sections
Here is a graphic that I hope will explain the overall structure of the animation. There will be three main sections: a contextual section, an ontogenic section, and a cinematic or environmental section. 

Hours

Setting up Wordpress 2 hrs

Troubleshooting Workflow 2 hrs

Presentation Prep 2 hrs

Research & Reading 2 hrs

DIGM 620 - Week 5 Review

Here is a piece of concept art trying to depict the mass-mortality event. Here juveniles are trapped in a rapidly disappearing pool.

Here is one of the adult specimens that I generated photogrammetrically.

Here is a look at a slab of juveniles from the 123D Catch Desktop Interface.

Dave had suggested I invest a little more time into R&D of the rig to facilitate development down the road. Here I've modeled a very simple Bothriolepis in order to test out some of the properties of the hybrid animation/ontogenic rig.

Here are some rough anatomical sketches. I'm just trying to get aquatinted with all the armor plates and their positions.

Hours:

Meeting with Dave (.5 hr)
Meeting with Stefan (.5 hr)
Attempts to use ARC3D Serive (1 hr)
123D Processing (1 hr)
Concept art (3 hr)
Prototype rig (2 hr)
Readings (3 hr)

DIGM 620 - Week 4 Review

Last Thursday I visited Dr. Daeschler at the Academy in order to begin scanning the specimens. I'm still sifting through the files to access their usefulness, but I think overall it was a successful session. What I didn't realize was how physically intensive photogrammetry can be (see the video below). 

Photoshoot:
11 specimens 
1322 photos
3.85 GB

My setup

Hours:

Concept Art (3 hrs)

Storyboards (2 hrs)

Photoshoot @ the Academy (3.5 hours)

Uploading photos to 123D Catch  (2 hours)

DIGM 620 - Weekly Update

DIGM 620 - Workshop Project Pitch

Click here for google document

This Week's Activities:

- Readings (3 hr)
- Visual Reference gathering (2 hr)
- Writing & Blogging (2 hr)
- Exploration of 123D Catch software (2 hr)
- Setting up time for photo-shoot @ the Academy (0.5 hr)
- Met with Dr. Stefan Rank & Requested that he act as my advisor (0.5 hr)

Readings:

Northcut, K. "Insights from Illustrators: The Rhetorical Invention of Paleontology Representations", Technical Communications Quarterly, 2011

Cain, V. "The Direct Medium of the Vision: Visual Education, Virtual Witnessing and the Prehistoric Past at the American Museum of Natural History, 1890-1923", Journal of Visual Culture, 2010

Sigwart, J. "Crystal creatures: context for the Dublin Blaschka Congress", Historical Biology, 2008.

"Placoderms (Armored Fish): Dominant Vertebrates of the Devonian Period

Upcoming:

-Photoshoot @ the Academy
-Generating concept art & storyboards
-Arrange to borrow diffuse lights from DIGM

DIGM 620 - Week 2

Generated using photogrammetry

For this class project, I would like to practice generating 3D digital models from source fossils using digital photogrammetry. 

Recent years have seen an increase in the adoption of digital tools by paleontologists. What was once a discipline that relied solely on shovels, picks, and brushes has become one that actively utilizes 3D scanning, 3D printing, biomechanical modeling, and animation. Creating 3D models of fossils has opened up many new possibilities for both research and outreach.

On a practical level, digitization can reduce some of the inconveniences and risks of working with fossilized objects. It can minimize the number of times a potentially fragile specimen needs to be handled. It is also much easier to manipulate and pose a large specimen in digital space.

Digital models can facilitate the sharing of specimens between researchers. Previously if a researcher wanted to study a specimen from a collection in another part of the world, he or she would either have to travel to that institution or request that the samples be shipped. Shipping a physical fossil always comes with risks. The advancement of the internet now allows digital models to be easily viewed, hosted, and shared between individuals.

My current focus is on how fossil collections and the exciting science surrounding them can be made more accessible to the public. The fossils on display in a museum are only a small fraction of their total collection. The vast majority of the fossils are sitting in specimen cabinets behind the scenes. Some of these collections are significant findings with wide-reaching implications for the subject of evolution, ecology, development, and more. Due to fragility or impracticality, a great deal of these collections are generally off-limits to the public. 

There is a growing movement to digitize collections for preservation, integration of data, and to benefit the public. Many museums and institutions are starting to host their specimen catalogues for public viewing. Some are even sharing 3D models. 

C-T scanning and laser scanning are currently the most prominent techniques for bringing a fossil into 3D digital space, but these often require expensive equipment and software. I would like to explore the possibilities of an alternate technique known as photogrammetry. Automated digital photogrammetry software sifts through a series of photographs of an object, picks out overlapping regions, and generates a 3D point cloud which then can be transformed into 3D geometry. Of all the techniques, photogrammetry is currently the most cost-effective way to scan fossils. It is a useful technique because the only major piece of equipment required is a camera, there are several free services available, its resolution is comparable to other techniques, and it generates texture maps in addition to geometry. 

I currently have permission to scan a collection of Devonian placoderm fish, called Bothriolepis, at the Academy of the Natural Sciences. This collection will likely play an important role in my eventual thesis project (more on that in a later entry). Having polished digital models of these fossils will be a useful asset down the road.

I will be using Autodesk's free 123D Catch service  and software to generate models. I have performed a few guerrilla photoshoots to test out the feasibility of the technique. The two examples are available below (using the service p3d.in)

Here's an eagle statue near the steps of the art museum:
http://p3d.in/D2GFW

Here's a Chasmosaurus skull from the Academy:
http://p3d.in/VALel

I was surprised by how much it was able to catch. The areas that were in shadow lost a lot of detail though, but could be fixed with proper lighting (The Academy is pretty dim). Also, occluded regions (back of the frill) were lost.

The project will serve to both generate stand-alone digital models, produce assets to serve as reference material for my thesis project, and to gain further familiarity with the photogrammetry work flow.

Some of the challenges I will be facing include: camera-related distortion, capturing fine-details on surfaces, post-work, capturing occluded regions, cleaning up digital artifacts and holes, retopologizing, avoiding 'digital erosion', transferring texture information onto UV-maps, and poly-reduction. 

Proposed Deliverables:
- A series (3-4) of digitized 3D fossils presented either through an animated turntable or embedded in a website. 
- (tentative) A tutorial video discussing the workflow. 

This Week's Activities:
- Meeting with Dave Mauriello to discuss project and research question (1 hr)
- Web stream of iDigBio Paleontology Digitization Workshop  (2 hrs)
- Setting up Blog (2 hr)
- Introduction Entry (1 hr)
- Pitch Entry (1 hr)
- David Wagner talk @ ANS regarding American Wildlife Art (1 hr)
- Misc Reading (3 hr)
- First fieldwork day at Inversand dig site (ENVS 865 - Field Methods in Paleontology)

Readings:

Min Zhu et al. "A Silurian placoderm with osteichthyan-like marginal jaw bones". Nature, 2013.

Werdelin, Lars, and John A. Long. "Allometry in the placoderm Bothriolepis canadensis and its significance to antiarch evolution." Lethaia, 1986

Cloutier, R. "The fossil record of fish ontogenies: insights into developmental patterns and processes." Seminars in cell & developmental biology. Academic Press, 2010.

Wells, N. A., and J. A. Dorr Jr. "Form and function of the fish Bothriolepis (Devonian: Placodermi, Antiarchi): The first terrestrial animal." Michigan Academician, 1985.

Janvier, Philippe, Sylvain Desbiens, and Jason A. Willett. "New evidence for the controversial “lungs” of the Late Devonian antiarch Bothriolepis canadensis (Whiteaves, 1880)(Placodermi: Antiarcha)." Journal of Vertebrate Paleontology, 2007

Goujet, Daniel. "“Lungs” in Placoderms, a persistent palaeobiological myth related to environmental preconceived interpretations." Comptes Rendus Palevol, 2011.

All Your Yesterdays: Extraordinary Visions of Extinct Life from a New Generation of Paleoartists, Irregular Books, 2013;

Expected activities:

Coordinate with Dr. Daeschler and plan first photoshoot @ the Academy

Contact Jason - to see if I can get 123D Catch installed on one of the lab PCs. 

Young, Gavin C. "Placoderms (armored fish): dominant vertebrates of the Devonian Period." Annual Review of Earth and Planetary, 2010