CBRC Digital Repository: Storing and viewing 3D objects, for science!

James HallidayProgrammer/Analyst, Library Technologies

Juliet L. Hardesty (@jlhardes)Metadata Analyst, Metadata Resources & Systems

Indiana University LibrariesDigital Library Brown Bag, October 7, 2015

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CBRC

• Center for Biological Research Collections• Specimen collections– Herbarium - 2D plants– Paleontology and Zooarchaeology – 3D bones– 10’s of K’s of items

• Specify Software– Specimen management and cataloging– Darwin Core, geospatial info

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flickr

flickr

BonesBones & Plants

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Bones & Plants

Various marmot bones from Mineral Hill Cave,US Dept. of Interior Bureau of Land Management

CBRC Member Collection, Indiana University Herbarium

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3D Bones

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CBRC Needs

• Cataloging and inventory management covered

• No place to store/preserve images• No way to provide public access to digitized

specimens

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What IU Libraries will provide

• Workflow for multiple file types (.tif, .stl, .zip)• Possibility of system mostly out of the box that

lets collection managers actually manage collections in Fedora– Type of collection (specialized metadata)– 3D images– New things we haven’t managed previously

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Darwin Core metadata

• All CBRC collections use the Darwin Core metadata standard

• Extension of Dublin Core to add metadata specific to biological collections

• See http://rs.tdwg.org/dwc/

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3D viewer integration

• 3D scans can currently be viewed using solutions such as SketchFab – see https://skfb.ly/CUqJ

• Adobe Acrobat PDF viewer• We hope to instead integrate a viewer

solution with Sufia using technology being developed at IU’s Advanced Visualization Lab

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3D printing at IU

Equipment, 3D Printing Studio, Indiana University

New 3-D printing lab in Wells Library open to IU employees, students, Inside IU, Sept. 30, 2015

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What is Sufia?

• https://github.com/projecthydra/sufia • Hydra-based institutional repository software• Based on Hydra infrastructure (Fedora backend,

Blacklight-based Rails frontend)• Primarily based around self-deposit• Originated as ScholarSphere at Penn State (

https://scholarsphere.psu.edu/) • One of the most polished and well-developed

Hydra projects

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ScholarSphere#dlbb

Sufia, Hydra and Fedora 4

• As a Hydra project, Sufia uses Fedora as a backend (http://fedorarepository.org/)

• Fedora 4 is a drastic restructuring of Fedora, making it cleaner and leaner

• Fedora 4 uses primarily RDF metadata• Sufia 6 uses Fedora 4, and is one of the first

Hydra projects to fully move to Fedora 4

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CBRC – why Sufia 6?

• Migrations from Fedora 3 to Fedora 4 are tricky, due to drastic differences between the versions

• CBRC data is all new, allowing us to create a Fedora 4 repository from scratch without worrying about migration

• Sufia meets most of the needs of the CBRC project out of the box

• Some features such as batch ingest still need to be added by local developers

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The Future of Hydra and Fedora at IU

• For now, our Sufia repository is specific to the CBRC collections

• It also serves as a pilot project for Fedora 4• Eventually, we might use a single Sufia instance to

hold a wider variety of content• Existing IU projects that currently use Fedora 3 will

eventually be migrated to Fedora 4• Potentially, non-Fedora projects (such as our DSpace

installations) might be moved to Hydra/Sufia

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Sample Item – Canis familiaris mandible

• Sample item from one CBRC collection– https://skfb.ly/CUqJ

• 3D images created using FARO ScanArm equipment• Each item will be digitized and stored in Sufia /

Fedora along with associated metadata• Metadata will also be stored in Specify, an open-

source Java-based platform for storing information about biological research collections (see http://specifyx.specifysoftware.org/)

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Sample Item in Specify

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Specify Taxonomy Tree

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Sample Item in Sufia#dlbb

Sample Item in Fedora

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Specify and Sufia work together

• All metadata stored in both Specify and Sufia• Specify provides data entry and analysis tools

that would be hard to replicate• Data synchronization is an issue• Sufia serves as the primary archival location

for both data files and metadata

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Batch ingest and workflow

• We need automated scripts between the digitizers workstations, Sufia and Specify

• We will leverage existing infrastructure for image processing and backup as much as possible

• 2D image creation will follow the usual process, but 3D image creation is new

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3D file issues

• No existing standards for 3D preservation and access

• 3D imaging produces multiple files per object• Archival files are quite large, but a smaller

‘derivative’ file can also be generated• Might need to allow more than one 3D scan per

object• Web access to 3D object might be accomplished

through a plug-in

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Thanks! Question? Comments?

• Github repohttps://github.com/IUBLibTech/cbrc

• Jim Hallidayjhallida@indiana.edu

• Julie Hardestyjlhardes@iu.edu @jlhardes

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