3D Digitization of the NHMLA Vertebrate Fossil Type Collection

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Biography

Dr. Carmen Obied and Steven Lopez are Maritime Archaeologists and Photogrammetrists with a PhD and MSc respectively from the University of Southampton, England. They are also Certified Scientific Divers with the American Academy of Underwater Sciences (AAUS) and the European Scientific Diving Panel (ESDP). They have over a decade of experience conducting international maritime and terrestrial archaeological excavations, geoarchaeological and geophysical surveys, as well as managing photogrammetry, GIS, and outreach projects. Their work has taken them to places such as the UK, US, Egypt, India, Oman, Spain, and the Balkans. They have collaborated with research institutions, governmental agencies, outreach organizations, and museums such as the Natural History Museum of Los Angeles County (NHMLA), British Museum, Mary Rose Museum, and the Western Australian Museum. Currently they develop 3D photogrammetric models for NHMLA, provide archaeological Cultural Resource Management for FirstCarbon Solutions, and act as Expert Archaeologist & Presenter for Past Preservers media agency for scientifically informed documentaries for educational outreach.

Vanessa Rhue and Dr. Samuel McLeod are Collections Managers in the Vertebrate Paleontology department at the Natural History Museum of Los Angeles County (NHMLA). Vanessa became interested in photogrammetry as a documentation technique when a workshop was offered on the topic at the Society of Vertebrate Paleontology meetings in 2013. She has over a decade of field, lab, and collections experience in Southern California and is an active member of the paleontological community, serving as Co-Chair of the Preparator’s Committee for the Society of Vertebrate Paleontology (SVP) and as Vice President for the Association of Materials and Methods in Paleontology (AMMP). Dr. McLeod received his PhD in Paleontology from the University of California Berkeley where he joined the pioneers in constructing digital databases for Vertebrate Paleontology collections. At the NHMLA he resurrected the Rancho La Brea digital database records that had initially been captured in the 1960s in what was probably the first Vertebrate Paleontology collections digitization project sponsored by the National Science Foundation (NSF). Subsequently Dr. McLeod received an NSF grant to digitize NHMLA Vertebrate Paleontology specimen and locality records and managed the NSF grant to digitally capture the data for the NHMLA Invertebrate Paleontology collections.

Project Background

The Vertebrate Paleontology (VP) department at the Natural History Museum of Los Angeles County (NHMLA) set out to increase online digital access to their type collection for both researchers and the general public. A type specimen is the name bearing specimen of a species new to science. The NHMLA Vertebrate Paleontology collections number over 160,000 cataloged specimens of fossil sharks, fish, reptiles, amphibians, birds, and mammals. Of these, there are over 1,100 primary type specimens, including holotypes, paratypes, neotypes, and syntypes. While 74 type specimens had been digitally imaged, the JPEG files were only previously discovered for viewing and download via the department’s Collections Search Form. Now people around the globe can interact with 3D models of holotype specimens from the VP collections, along with a description of the taxon name, location, age, and scientific publication citation.

The former user experience of 2D images via the VP Collections Search Form.

The new interactive user experience of 3D models via Sketchfab

We were attracted to the goals of the project and partnered with the museum team to apply our knowledge of photogrammetry to their data set. We joined the project in 2016 and began by developing a workflow which identified the holotype specimens of amphibians and reptiles as the first vertebrate classes to prioritize for 3D modeling. Our training in 3D modeling first began a few years ago at the University of Southampton, England where we documented shipwrecks and artifacts using DSLR cameras and Agisoft PhotoScan software primarily, with Sketchfab as a platform for showcasing the 3D models. While the scale of the object being imaged has changed, the techniques and processes are similar. We enjoy taking on new challenges and developing solutions to tricky imaging situations – whether it is changes in light underwater or carefully mounting a tiny skull of a fossil lizard. Sketchfab serves as a valuable platform to engage a broader audience with our models so that people around the globe can discover, interface, study, and learn about these scientifically significant, yet not as well-known, paleontological specimens.

3D Models: Purpose & Technique

LACM 103351, Euclastes hutchisoni, Skull in left lateral view as seen in different phases of processing with Agisoft PhotoScan Pro (right to left: sparse point cloud, dense point cloud, surface model, textured surface model).

We appreciate the value of 3D models for both educational and public outreach purposes, as well as scientific and academic research. While there are many ways to produce 3D models, we’ve chosen to use photogrammetric techniques. Photogrammetry is the technique of generating precise mathematical measurements and three-dimensional data from two-dimensional photographic image sequences that exhibit stereoscopic overlap (see BLM Technical Note 428 and Journal of Paleontological Techniques No. 12). We accomplish this by taking high quality digital images of the specimen and process those files using Agisoft PhotoScan Pro to render 3D models by merging chunks of data, generating a dense point cloud, creating a polygon mesh frame, and applying a vivid texture. These steps result in an image-based 3D model than can be viewed and manipulated on the x, y, and z axes.

Some of the benefits of creating 3D models with this non-invasive technique extend to various research, education, and object conservation sectors, including:

  • Remote Viewing & Increased Accessibility
    • The specimen can be accessed and viewed remotely via online platforms, shared as a PDF file between colleagues, or incorporated into an exhibit display kiosk. This decreases the need for museums to issue hand carried loans and increases access to important comparative materials. Increased awareness and accessibility to the collection is also made possible to a broader audience than the scientific community, allowing for an array of public education programming.
  • Digital Manipulation & Documentation
    • The specimen can be digitally manipulated along the x, y, and z axes without physical handling. This decreases the odds of physical damage to the specimen during study. 3D models also serve as a digital record of the specimen’s condition at a given point in time, becoming valuable to the scientific community should the specimen become lost or damaged.
  • Digital Reproduction & Exhibit Display
    • The specimen can be digitally reproduced instead of being subjected to the physical forces of traditional molding and casting techniques. This can be useful for exhibition, exchanges with other institutions, and, as the quality of 3D printing continues to improve, it may also prove useful for research study.
  • Digital Public Engagement
    • Photogrammetry is increasingly becoming a widespread practice within the scientific community. The routine data capture of high quality digital specimen images coupled with affordable access to processing software have been driving forces behind the ever-growing virtual museum. This type of digital public engagement allows researchers and the general public to interact with rare specimens that would otherwise be distant and obscure from their day to day experiences. 3D models can be accessed by people without the means or ability to physically visit a museum. The models can also enhance and complement a museum exhibition by allowing certain angles and details to be highlighted that wouldn’t otherwise be exposed. The models can also be viewed in VR, enhancing the interactive user experience. It can also serve as a useful pedagogical tool for lectures and educational use in schools and universities.

At NHMLA we supplement our digital image library of 2D pictures with 3D photogrammetric models, which offer a more comprehensive view and record of the specimen for posterity. We’re also aiming to attach PDFs of the models as multimedia records to our internal specimen database so that the files can be more centrally accessed by staff. We’ve appreciated the benefits of remote viewing and digital manipulation for increased accessibility to our research community and the general public. We’ve been able to send files of 3D models to colleagues remotely so that they can be apprised of the latest information revealed by further preparation of a specimen. We can also embed the 3D models on our museum website or link visitors to our department website from Sketchfab. Although we’ve yet to create 3D prints using these files, that’s a future direction we can explore for upcoming exhibit displays or loans. One of the most rewarding benefits has been to watch children and adults of all ages engage with the models during museum outreach events via handheld tablets and loop video clips. Watching the expression on people’s faces as they digitally interact with a type fossil from our museum collections is riveting – it brings the science alive in a personal way!

How-to Guide

There are two main components to creating 3D models using photogrammetric techniques. The first is image data capture and the second is image data processing. The key to rendering high quality 3D models is starting with a series of good quality digital images. The importance of basic DSLR photography skills cannot be overstated. Establish a standard workflow for digitally imaging specimens with photogrammetry image processing in mind. Once the data is captured, you’ll be able to use those images for processing later on – whether it’s weeks or years down the road.

Photogrammetry Workflow

1. Specimen Selection & Approach

For this project, we choose to prioritize the holotype specimens by vertebrate class, starting with fossil amphibians and reptiles. Within each group, we individually assessed the physical traits of the specimen and the workspace constraints. Here are some things to keep in mind:

  • What is the specimen’s location, size, weight, and shape? This may influence where the photoshoot can take place (e.g. indoors versus outdoors, or on a desktop, roundtable, or floor).
  • How should the specimen be handled and supported? For example, can the specimen be safely mounted to a turntable? Should the specimen remain fixed and the camera hand-held or can the specimen be rotated on a turntable while the camera remains fixed to a tripod?
  • What is the natural lighting situation? For example, will the specimen fit into a light box with or without fluorescent or LED lighting? Can the specimen be shot in natural light? Are shadows obscuring important morphology? For this project, whenever possible, we shot specimens mounted to a turntable placed inside a lightbox lit with florescent lights from the top, left, and right.
  • What are the foreseeable challenges to imaging the specimen and/or what are the workspace constraints? For example, is the specimen fixed to an exhibit mount behind glass? Is the specimen too fragile to withstand frequent handling and positioning? Is a ladder required for imaging large specimens to avoid image distortion?

Challenges will arise from time to time. Be flexible and make adjustments to your workflow as needed.

Tip: Designate a permanent photography space for the project. Having your photo station set up with all your needed equipment and optimal conditions will greatly improve the efficiency and quality of your data capture – plus other visiting researchers, volunteers, and staff can utilize the photo studio too!

The fossil holotype skull of LACM 13739, Pumilia novaceki, is mounted vertically to maintain a consistent focal distance when rotated for imaging on a turntable.

2. Digital Image Capture

  • Shoot in Manual and use RAW file format for image capture
  • Keep ISO as low as possible to limit digital noise (e.g. ISO 100-200)
  • Take photos with good depth of field (e.g. Aperture f16)
  • Use an appropriate shutter speed for handheld versus tripod photography (e.g. 1/200th – 1/1,000th of a second)
  • Include a scale bar (object of known length) and/or coded targets in the image footprint
  • Maintain the same focal length and focus distance throughout the photo series
  • Maintain 60% stereoscopic overlap between photos in the series
  • If needed, oblique photos taken at a high angle are better than a low-angle to provide maximum stereoscopic overlap

An average of 70-150 images (depending on the specimen size) were captured in a series to generate these 3D models.

3. Image Editing

If necessary, the RAW images were edited using Adobe Photoshop prior to processing, which usually involved a combination of brightness, contrast, and sharpness in order to clearly distinguish the object from the background. The images were then saved as TIFF or JPEG files. The format choice is dependent on various factors, but for the highest level of detail select TIFF.

Carmen Obied manipulates a PDF version of a 3D model created for a Curator’s research project.

4. Image Processing

  • In-program data setup
  • Import and align photos including spare point cloud generation and clean-up
  • Dense point cloud generation (may be skipped if a polygon mesh is to be calculated. However, meshes from dense clouds are usually superior)
  • Polygon mesh generation (optional)
  • Texture generation (optional)
  • Data export: you can export the completed model as an OBJ file, which can then also be uploaded into Sketchfab. You can also export the model as a PDF file and other formats.

Steven Lopez examines the finished 3D model of the fossil holotype skull of LACM 103351, Euclastes hutchisoni, in Agisoft Photoscan Pro.

For step-by-step instructions on how to process image data, we recommend downloading the Agisoft PhotoScan software user manuals and tutorials.

Photography Equipment:

  • DSLR Camera with full frame sensor
    We used a Canon EOS 5D Mark II body with a 24-70 mm lens
  • CF or SD Memory Card (16-32 GB minimum) and card reader
  • Fully charged battery and/or spare battery with charger
  • Coded targets
  • Photographic scale (ideally with color calibration)
  • White manual turntable (Lazy Susan)
  • 16” cube light tent with 3 fluorescent lights on stands (85W bulbs)
  • Selection of small boxes, foam pieces and/or plastalina modeling clay
  • Optional: Remote Switch and USB cord for tethering to your computer, light bounce reflectors

Hardware:

Agisoft PhotoScan recommends these minimum system requirements:

  • PC or Mac Computer with image-processing capabilities
  • CPU: Quad-core Intel Core i7 CPU, Socket LGA 1150 or 1155 (Kaby Lake, Skylake, Broadwell, Haswell, Ivy Bridge or Sandy Bridge)
  • Motherboard: Any LGA 1150 or 1155 model with 4 DDR3 slots and at least 1 PCI Express x16 slot
  • RAM: DDR3-1600, 4 x 4 GB (16 GB total) or 4 x 8 GB (32 GB total)
  • GPU: Nvidia GeForce GTX 980 or GeForce GTX 1080 (optional)

Software:

There are numerous software packages available for photogrammetric processing on market. We used Agisoft PhotoScan Professional.

A fossil shark tooth of Carcharocles megalodon, as mounted on a plastalina clay base atop an automatic rotating turntable with coded targets and scale.

3D Models on Sketchfab

NHMLA 3D Models of Holotypes on Sketchfab:

Future of 3D in Cultural Heritage

High resolution 3D models provide a dynamic interface for researchers to gather data from complex anatomical structures like a skull than could otherwise be accomplished with traditional 2D photographs. By using 3D modeling and platforms such as Sketchfab, we are able to reach and engage with a wider audience that goes beyond the scientific research community, including public and educational engagement. For example, at a recent museum public outreach event guests were able to view and interact with a 3D model using a tablet. Additionally, workshops serve as a useful means of gaining both a theoretical and practical understanding of the best photogrammetric practices to ensure high-quality digital images are captured for the rendering of scientifically accurate 3D models with a mesh frame and vivid texture. In the field of paleontology and cultural heritage there are different photogrammetric approaches and a variety of software options available. Check out the North American Paleontological Convention to be held in June 2019, where we will be leading a workshop on photogrammetry that will offer a practical overview of the methodological approaches and equipment used in photogrammetry. We’ll be highlighting this holotype project as a case study, as well as conveying other scientific applications to the curatorial process and the outreach benefits. Through 3D cultural heritage, we hope to encourage the widest possible use of museum collections – both digitally and physically.

Ultimately, the photogrammetric process acts as a powerful tool for museum conservation and outreach purposes and 3D Imaging will soon become an essential component of cultural heritage and museums, particularly within the areas of documentation, conservation, and interpretation. Current research and projects are paving the way for further discussion as to how these technologies can be best incorporated into cultural heritage and pedagogical practices.

Stay tuned for more 3D models of fossil holotypes!

  • Chondrichthyes – cartilaginous fishes
  • Osteichthyes – bony fishes
  • Aves – birds
  • Mammalia – mammals

Additional models forthcoming to Sketchfab may include those generated by researchers who visit the museum’s collections. Portable 3D scanners, such as Go!Scan 3D, and processing software such as VXElements and Geomagic Wrap have recently been used to capture 3D data.

Acknowledgements

This research has been supported by various people in the Natural History Museum of Los Angeles County throughout its development, and we would particularly like to thank Dr. Samuel A. McLeod and Vanessa R. Rhue for their continued support of this photogrammetric project.

Dr. Carmen Obied’s Website / Steven Lopez’s Website / Natural History Museum of Los Angeles County

About the author

Carmen Obied, Steven Lopez and Vanessa Rhue

The 3D models of holotype fossils uploaded to Sketchfab are the result of photography and processing work by Dr. Carmen Obied and Steven Lopez, MSc. The project is overseen and managed by Vanessa R. Rhue and Dr. Samuel A. McLeod.


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