3D Scanning the D’Arcy Thompsons Zoology Museum Collection

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This post is by community member Dr Caroline Erolin, published by Sketchfab staff.

My name is Caroline Erolin and I am a lecturer in Medical Art at the University of Dundee in Scotland. During 2016 I was lucky enough to lead on an exciting project involving the digitisation of specimens from the University’s Zoology Museum. The Zoology Museum houses many fascinating specimens from around the world. Most of them were collected by the celebrated Sir D’Arcy Wentworth Thompson, the first Professor of Biology at Dundee. 2017 is the centenary of D’Arcy Thompson’s influential book On Growth and Form and a number of events will be taking place around the country to celebrate.

I became involved in the project after visiting the museum with the MSc Medical Art students whom I teach. The Centre for Anatomy and Human Identification (CAHID) where I work had recently purchased two new structured light scanners (an Artec Eva and Artec Space Spider) and I was keen to put them to the test. I had also recently been trained to use the University’s new microCT scanner (a Nikon XT H 225ST). The project seemed the perfect opportunity to hone my 3D scanning and modelling skills.

I worked on the project throughout 2016 whenever the opportunity arose between teaching and completing my PhD (in Medical Visualisation). Smaller specimens were scanned with the microCT scanner (figure 1), while larger specimens were captured using the Artec scanners (figure 2). A major advantage of the microCT scanner is that it can achieve very high levels of detail as well as capturing internal structures. The disadvantage however is that no colour information is obtained. This had to be added manually during  the post processing stage using ZBrush. Larger specimens were scanned using either the Artec Space Spider or the Artec Eva scanners in conjunction with Artec Studio 11 professional software. In contrast to the microCT scans, the surface scans did capture colour texture which was exported along with a UV map and obj to ZBrush.

The majority of the post processing occurred within ZBrush. This was similar for both the microCT and surface scans. All of the scans needed their geometry ‘tidying’ to some degree by deleting any unnecessary data and artefacts as well as repairing and remodelling any missing data. The meshes were then retopolgised using the Dynamesh feature to reduce the polycount and optimise the geometry. It was not possible to create UV maps for the scans from the microCT, as even when simplified greatly, the mesh was too complex to unwrap. Likewise, although the surface scans were initially imported with a UV map, this was lost when the geometry was tidied and retopologised. As such, a balance had to be struck during the dynameshing process, so that the models would not be too large to load on Sketchfab but would not lose too much detail either.

To texture the microCT scans, good quality photographs were taken of the specimens which were used with the ‘Spotlight’ and ‘Polypaint’ features of ZBrush. The Artec scans came with texture maps which were converted to Polypaint to be further edited (corrected for harsh shadows etc.,) along with the geometry. As Sketchfab is capable of loading the vertex colours associated with the obj file, it was not too much of a problem that UV and texture maps couldn’t be created. The only slight issue being that for the colour textures to look sharp, the polycount of the models had to stay reasonably high, usually between 400,000 and 1 million. This could result in longer loading times which would be problematic on older or lower powered devices. In order to compensate for this, the larger models were duplicated at a lower polycount and labelled as being for mobile devices.

All the models were uploaded to Sketchfab directly from ZBrush using the exporter plug in. Sketchfab was chosen as the platform to host and distribute the models due to its ease of use and support for cultural heritage institutions. The University of Dundee Museum Services were provided with a free Business account under the user name of ‘University of Dundee Museum Collections’.

Within Sketchfab the ‘3D settings’ tab was used to optimise the appearance of each model. A custom background featuring the University and Museum logos was also added. The ‘Properties’ tab was used to add a detailed description of the specimen along with how it was scanned and processed. All of the models were made available for download under a Creative Commons attribution, non-commercial, share alike license.

To date, the Sketchfab site has over 350 followers with the models having received over 15,000 views from more than 25 countries, with over 2500 downloads having taken place. The project has also led to several exchanges with external researchers. For example, a researcher in Integrative Biology from the Conway Institute of Biomolecular and Biomedical Science at the University College Dublin contacted us about the Blaschka glass models, to inform us that they had been wrongly labelled and to share with us information regarding D’Arcy Thompson’s original order of models in 1888.

Another expert contacted us regarding the identification of the Elephant skull. This had previously been thought to be that of an Indian Elephant, but we were informed that it actually belonged to an African Forest Elephant (Loxodonta cyclotis).

The final stage of the project was to create a webpage to showcase the models.  The landing page features thumbnails of all available scans , which when clicked take the user to a page containing the 3D model and information about the specimen. The site went live in January 2017.

While the main body of work is now complete, it only represents a tiny fraction of the estimated 4,200 specimens in the collection. However, we are encouraging our students (such as those on our MSc in Medical Art) to get involved with scanning more specimens so that the collection will continue to grow.

Be sure to check out all of the awesome zoological scans on the University of Dundee Museum Collections’ Sketchfab profile.

About the author

Thomas Flynn

Cultural Heritage Lead at Sketchfab.
Co-founder of museuminabox.org


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