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Digital Applications in Archaeology and Cultural Heritage 7 (2017) 51–55

Contents lists available at ScienceDirect

Digital Applications in Archaeology and Cultural Heritage
journal homepage: www.elsevier.com/locate/daach

Zoology 3D: Creating a digital collection of specimens from the D′Arcy T
Thompson Zoology Museum

Caroline Erolina, , Matthew Jarronb, Laszlo J. Csetenyic
a
Centre for Anatomy and Human Identification, University of Dundee, Dundee DD1 5EH, Scotland, UK
b
Museum Services, University of Dundee, Dundee DD1 4HN, Scotland, UK
c
School of Science and Engineering, University of Dundee, Dundee DD1 4HN, Scotland, UK

A R T I C L E I N F O A B S T R A C T

Keywords: The University of Dundee's D′Arcy Thompson Zoology Museum houses many fascinating specimens from around
Digital the world. Most of them were collected by the celebrated mathematical biologist Sir D′Arcy Wentworth
microCT Thompson, the first Professor of Biology at Dundee. 2017 sees the centenary of the publication D′Arcy
Museums Thompson's extraordinary book On Growth and Form. During 2016 a project to digitise key specimens from the
Scanning
collection was undertaken as part of the centenary celebrations. Smaller specimens were scanned using a
Virtual
microCT scanner, while larger specimens were captured using hand-held structured light scanners. The resulting
Zoology
3D models were further processed using the software ZBrush before being hosted online via Sketchfab. They
were subsequently embedded on a bespoke webpage (https://www.dundee.ac.uk/museum/collections/zoology/
zoology3d/) as an extension of the existing University Museum Services website. This article goes on to discuss
the resulting collaborations and benefits of sharing museum collections online.

1. Introduction & context wider access, key specimens were digitised during 2016 with a view to
making them available online. The range of specimens chosen re-
Sir D′Arcy Wentworth Thompson (1860–1948) was a Scottish presents both the diversity of the collection as well as the connection to
biologist and classics scholar. At the age of 24 he took up the first Chair D′Arcy Thompson and his work. For example, the Emperor Penguin
of Biology at what was then University College, Dundee in 1885. During (https://skfb.ly/PNTt) was brought back for him from the Dundee
his 32 years in Dundee he founded and developed a large and im- Antarctic Expedition of 1892, and is thought to be one of the oldest
pressive Zoology Museum, collecting specimens from around the world. specimens in existence. The Musk Ox (https://skfb.ly/PKwW) and
Although this building was demolished in the 1950s, a new museum Walrus (https://skfb.ly/PNuQ) are examples of specimens collected by
housing many of the surviving specimens was opened in 2008 at the the Dundee whalers in the Arctic, while the Sea Otter (https://skfb.ly/
University of Dundee. Thompson's collection helped to inform his OPMV) was an animal whose population decline Thompson highlighted
ground-breaking research into the mathematical principles of nature, as part of an international inquiry. The Nautilus shell (f https://skfb.ly/
which culminated in the 1917 publication of his landmark book "On VuLL) is perhaps the most iconic example of his interest in mathema-
Growth and Form" (Thompson, 1917). This pioneered the science of tical growth patterns. Other specimens were chosen for different rea-
biomathematics and has been hailed as "the greatest work of prose in sons – the Thylacine (https://skfb.ly/OLUz) being selected by visiting
twentieth century science." (Gould, 1992, ix). 2017 sees the centenary artist Kelly Richardson as part of an art project involving extinct spe-
of this extraordinary book and such a number of events are taking place cies.
around the world to celebrate (https://www.ongrowthandform.org/). Over the last decade, 3D digital scanning of museum and cultural
The current Zoology Museum is used for a range of learning and heritage artefacts has become increasingly commonplace (Wachowiak
teaching activities within the University. It is open to the public one and Karas, 2009). Capture techniques vary and include 3D surface
afternoon per week during the summer as well as occasional open days scanners (Li et al., 2010), photogrammetry (Marine Fau et al., 2016)
such as at Easter and Doors Open Days. However, due to security and and clinical imaging techniques such as MRI and CT scanning (Zhang
academic requirements, it is not generally open outside of these times. et al., 2012). In addition, it is easier than ever to share these virtual
In order to both raise awareness of the collection, as well as to provide objects with an audience online. With over half a million users


Corresponding author.
E-mail addresses: c.d.erolin@dundee.ac.uk (C. Erolin), m.h.jarron@dundee.ac.uk (M. Jarron), l.csetenyi@dundee.ac.uk (L.J. Csetenyi).

https://doi.org/10.1016/j.daach.2017.11.002
Received 29 March 2017; Received in revised form 29 September 2017; Accepted 15 November 2017
Available online 20 November 2017
2212-0548/ © 2017 Elsevier Ltd. All rights reserved.

A major advantage of such scans is that feature to align them. The ‘Spotlight’ feature allows for photographs to be projected specimen. The Artec Space Spider or the Artec Eva structured light scanners. while larger specimens were captured using hand. This had to be added manually therefore within ZBrush.ly/VLwH)). Workflow the colour textures to look sharp. Sketchfab is now the most widely and painted directly on to the model (Fig.ly/PPNH).1. and setting the material properties to suit the ZBrush. Once fused. 2). the polycount of the models had to stay reasonably high.2 (and later When imported into ZBrush. A map size of 1024 × 1024 was used. The University of Dundee Museum Services were provided metry’ sub-menu.jpeg image required flipping vertically prior to loading within ‘surface extraction’ window.ac.obj file this was not a major problem. 3). MicroCT ccanning and post processing 2. Any resulting holes models due to its ease of use and notable support for cultural heritage were filled using the ‘close holes’ feature also within the ‘modify geo. On the few occasions where this wasn’t the 2000 × 2000 pixel flat panel detector. The Nikon XT H 225ST has a others this worked well.ly/OING) where visualisation of the internal structures Polypaint feature. while the colour useful for others specimens such as the Nautilus Shell and Prairie Dog texture was corrected for harsh shadows and missing data using the (https://skfb. So long as each scan had enough overlap with the they can achieve very high levels of detail. These images were paint missing textures’ selected. The only slight issue being that in order for 2. Despite retopologising about).3. Specimens > 250 mm in diameter were scanned using either the held structured light scanners (Artec Eva and Artec Space Spider). Good setting the field of view to around 30°. then sent to a 2nd computer (a high performance PC with a 24-core Once created. the quate 125 µm. but is better able to scan larger specimens creative commons licence. Over 500 cultural heritage institutions large and small have the models. Sketchfab missing data. the reconstructed volume contains texture’ feature) in order for it to be further edited along with the all the information of the interior structure. Unfortunately the process of tidying and re- was desired. moved closer to the Unlike the microCT scanner. This means The aligned scans were then fused using the ‘sharp fusion’ feature with that for very small specimens a resolution of a few µm can be achieved. This was crucial for wet geometry. non-commercial-share-a-like resolution of up to 0. resulting in a minimum of two Specimens < 250 mm in diameter were scanned using a Nikon XT H scans per specimen (Fig. Once in ZBrush the geometry of each model was ‘tidied’ by deleting any unnecessary data and artefacts as well as repairing and remodelling any 2. texture map was converted to Polypaint (using the ‘polypaint from In addition to the outer surfaces. which is positioned 1130 mm away from the source. they were reconstructed using VGStudio Max version 2. they remained too complex to create satisfactory UV maps joined to date from 51 different countries. two GTX970 graphics cards and 128 GB RAM) where as a.C. Both webpage (https://www. using the software Inspect-X. institutions.jpeg file. both Artec scanners were able to detector to fit in the frame) this drops to about a still more than ade.ly/Pv9M) and way as for the models from the microCT scanner.obj mesh Xeon processor. All scans used for the fusion were used for the texture.com/ feature allows for manual painting of the model. topologising the geometry resulted in the UV maps being deleted. They were subsequently embedded on a new such as the African Forest Elephant Skull (https://skfb. the models captured using the Artec using version 3. capable of loading the vertex colours associated with the.5 mm. These included: positioning the model and captured. usually between 400. Once uploaded to Sketchfab a number of parameters were altered A disadvantage of microCT scanning is that no colour information is using the ‘3D settings’ tab. The resulting 3D models (. where they were made available for viewing and down. over in order to scan all of the surfaces. for example a more matte finish was chosen for bone while a 52 . which recreates the surface with a more optimal Dundee Museum Collections’. All of the specimens scanned in this way required turning Services website. adding a custom background quality photographs were taken of all the specimens which were used to featuring the University and Museum logos. and as such they were uploaded to Sketchfab without.2. As Sketchfab is cultural-institutions-joined-sketchfab/). as Sketchfab supports.stl files) were imported into the 3D However.sketchfab. The Artec Eva can achieve a loading worldwide under an attribution. the ‘fill holes’ option set to ‘watertight’. measuring 400 mm × 400 mm case. The were captured using a tungsten reflection target as the specimens were options were left at their defaults with ‘generate texture atlas’ and ‘in- rotated through 360°. but for larger objects (up to 250 mm in diameter. texture was added to the models using the ‘texture’ tab within Artec To generate a 3D volume. Dolphin Skull (https://skfb. The models were uploaded directly from geometry that can also be set to a lower polycount where required ZBrush using the built in Sketchfab uploader. The Artec resulting 3D models were further processed using the 3D modelling Space Spider can achieve a resolution of up to 0.0) to generate 3D volumetric representations of the scanners came with ready-made UV maps allowing for the.1 mm and was used on software ZBrush before being hosted online via Sketchfab (https://skfb. in size.000 and 1 million. Unnecessary data and artefacts were deleted by first hiding the relevant part of the mesh and then selecting ‘delete hidden’ Sketchfab was chosen as the platform to host and distribute the 3D under the ‘geometry’ and ‘modify topology’ menus. It should be noted however that final surface which was exported as stereolithographic file using the the. while the ‘Polypaint’ used platform for distributing 3D content (https://sketchfab.dundee. Digital Applications in Archaeology and Cultural Heritage 7 (2017) 51–55 contributing over a million models. Erolin et al. (Fig.obj vertex colours this wasn’t con- modelling software Pixologic ZBrush (version 4R7) for post processing. applying standard studio texture the models using the ‘Spotlight’ and ‘Polypaint’ features of lighting across all models. Artec Studio 11 was used to first run fine 225ST microCT scanner based in the School of Science and Engineering and global registrations of the scans before using the ‘auto-alignment’ at the University of Dundee.com/500. The geometry was ‘tidied’ and retopologiesed in the same potted specimens such as the Pencil Urchin (https://skfb. 2. Structured light scanning and post processing Smaller specimens were scanned using a Nikon XT H 225ST microCT scanner. sidered to be a big problem. Once the models with textures were loaded into ZBrush the was used for all specimens. 1). specimens of up to around 60 cm (such as the Long-beaked Common ly/PpUo).jpeg file to specimens. The ‘surface determination’ feature was used to create the easily be added as the texture map. the texture maps were exported along with the. capture photographic texture in addition to geometry. making Sketchfab one of the (a UV map allows a 2D texture map to be projected onto a 3D image) largest virtual museums in the world (https://blog. scans could be manually aligned by selecting pairs of locations. The pre-set ‘normal with simplification’ ZBrush. a series of sequential 2D X-ray images Studio 11.uk/museum/collections/zoology/ scanners were used in conjunction with Artec Studio 11 professional zoology3d/) as an extension of the existing University Museum software. The meshes were then retopologised using the with a free Business account under the user name of ‘University of Dynamesh feature.

Erolin et al. was created as an extension of the existing University of Dundee Sketchfab allows for work to be easily shared under a Creative Museum Services website. In addition. two models. This process recreates the surface with a more optimal geometry that can also be set to a lower polycount. Once hosted on Sketchfab models As described in the sections above. The landing page features thumbnails of all Fig. the Blaschka Glass and the Prairie Dog Collections were made available for download under an attribution. This could result in longer loading times 2.ly/ Commons licence. the models were embedded within a bespoke webpage. Screenshot showing microCT of a Rhinocerous Beetle being textured using the ‘Spotlight’ feature of ZBrush which allows for pho- tographs to be projected and painted directly on to the model. colour texture was in the form on can easily be embedded on websites and social media and even vertex colour on the model itself rather than as a separate texture map. 2. 53 . This lower polycount and labelled as being for mobile devices. usually be- tween 400. microCT scan of a Rhinocerous Beetle before and after being retopologised using the Dynamesh feature within ZBrush. Digital Applications in Archaeology and Cultural Heritage 7 (2017) 51–55 Fig. share alike licence.C. This meant the polycount of the models was quite high.4. 3.000 and 1 million. Screenshot from Artec studio 11 Professional showing multiple scans. The four scans in this case are represented as an overlay of four different colours. the larger models were duplicated at a Finally. non-commercial. In order to compensate for this. downloaded for 3D printing. Fig. Results which would be problematic on older or lower powered devices. 1. were set to transparent. All models from the University of Dundee Museum OHHU). glossy finish was chosen for the Blaschka glass model (https://skfb.

available scans (Fig. 4). The The models are being used in a variety of learning and teaching site went live in January 2017 and can be viewed at: https://www. who are in- dundee. corporating them into their level three vertebrate anatomy and evolu- To date the Sketchfab site of the University of Dundee Museum tion module. Of the 41 models online. one is an (http://museuminabox. and the organisation ‘Museum in a Box’ who will be in- Collection has over 470 followers with 41 discreet models uploaded (to cluding one of the skulls in their school outreach program. 4. the project has also led to a number of exchanges from more than 25 countries. four are museum specimens are 3D printed and taken in to the classroom mounted skin preparations.ac. Screenshot of the landing page for the bespoke webpage. When these are clicked on. where date). initiatives including by the University of Queensland. a researcher in Integrative place. page containing the 3D model and information about the specimen. The collection has received over 20.1 M Science at the University College Dublin contacted us about the 54 . Erolin et al. Digital Applications in Archaeology and Cultural Heritage 7 (2017) 51–55 Fig.6 K vertices. with over 2000 downloads having taken with external researchers.000 views teaching activities. 20 are skulls.C. to the largest at 30. the user is taken to a Polygons / 1 M vertices. As well as being used for learning and insect. For example. 11 are Blaschka glass models. The model sizes vary considerably from the smallest at 963KB / Biology from the Conway Institute of Biomolecular and Biomedical 59. created as an exten- sion of the existing University of Dundee Museum Services website.uk/museum/collections/zoology/zoology3d/. The landing page features thumbnails of all available scans. and one is a shell. two are bones.7MB / 1.org/).2 K Polygons / 29.

students on the University of Dundee's MSc in ficult to learn. 221–225.. This could be reduced however if the textures were imported specimens to be added to the collection so that it might continue to and not altered. much of this time involves waiting for the software to run a actually belonged to an African Forest Elephant (Loxodonta cyclotis). Mus. The models could then be embedded on elephant and rhinoceros this isn’t practical and as such scale models our own web page by simply copying and pasting some html code. Hope Busak. Am.doi.2011. J.org/10. specimen. 3D Scanning and replication for Museum and cul- tural heritage applications.1016/j. Going ZBrush was variable and took between 30 min and two hours per spe- forward it is hoped that students will get involved in scanning more cimen. A cially the case where the texture is already captured either by the number of these students are already involved in producing more scanner or via photogrammetry. R. Gould. D. We are also sharing the raw CT data with them cimen. Sharing ma. H. S.J. or not-for-profit sectors. browser and https://sketchfab.doi. However. R. the degree to which the scans were ‘tidied’ and textured in tiny fraction of the estimated 4200 specimens in the collection.org/10. but they frequently host searchable databases of images and models and even complete virtual exhibitions. In Artec studio this could take up to an hour per Thompson Blaschka collection.doi. Zha. and is impacted by the graphics card and amount of RAM available. Use of microCT mounted skeletons: potential and limits. 1917. 381–388. This is espe- are trained in a variety of scanning and digital modelling modalities. will be produced. 3D printing of the specimens is Uploading editing the models on Sketchfab was quick and easy. pp. Cambridge. Botha. sing in ZBrush and using Sketchfab to host and embed models) could Wachowiak. However. which can be Zhang. to inform us that it had been wrongly labelled unattended. so other work can be carried on while this is taking place. assistant curator. Another expert contacted us regarding specimen as the aligning and fusing of scans could be time consuming the identification of the Elephant skull. but for much of this time the scanner could be left 55 .V.doi. process. In: terials in the way outlined here can greatly increase the visibility and Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). University of Dundee Museum 3. 2016). Herit. 'Introduction' to On Growth and Form. it is at Community 35. Erolin et al.. but we were informed that it However. Dik.2016. J.1016/J. grammetry (Marine Fau and Raphaël Cornette.J. Digital Applications in Archaeology and Cultural Heritage 7 (2017) 51–55 Blaschka glass model. however for some. http://dx.W. Ins. The role of the museum website is also changing. Canto ed. http://dx.C. depending on the complexity of the spe- order of models in 1888. 2010. This research did not receive any specific grant from funding No longer are they simply a source of visitor information regarding agencies in the public.. Cambridge University least equally important for smaller museums. A. The most time-consuming aspect of the workflow tended to be to assist in their research and endeavour to rebuild the D′arcy the post-processing.edu/ Dodge.. opening times etc.08. Raphaël Cornette. Cult.org/ reputation of a small museum.. First.003.004. M.. http://dx. it only represents a Finally.'S. This had previously been as. Discussion and outlook Services (2014–2016).org/10.. and over re- cent years the concept of what constitutes a visitor has been evolving. 13. These models will be used by Museum Services both for school outreach programmes and to allow visitors to the museum to Acknowledgments have hands-on experience of the objects. Funding Online visits to museum websites are now far outpacing physical visi- tation (Dodge. 968–977.. Robert Jackson and Alasdair Napier. 48.. sumed to be that of an Indian Elephant. 2016. 2012. In addition to the online material. Comptes Rendus Palevol 15. The models are being printed via the Sketchfab website. ed.5 h per radiation CT technology using open source and free software. It is hoped that the workflow presented can be used to help other Marine Fau. B... References Large museums such as the Smithsonian and British Museum have sizable collections of 3D models available online (https://3d. to be captured. limited opening hours to have a strong online presence. Technology — are museums keeping pace? MUSE Voice Can. The software described above is not particularly dif- grow. Process for the 3D used where scanners such as those used here are not available. especially those with Press. While the main body of work is now complete. J. virtual reconstruction of a microcultural heritage artifact obtained by synchrotron Setting up and taking the microCT scans took around 1. 〈http://dx.. 3D digitization and its applications in cultural heritage. Blaas. DJCADMake.si. J. T. such as the around another five minutes. underway. Luo. For example. added manually.. and Artec surface scanners allowed for particularly high-quality scans Thompson. Li. A. Cambridge University Press.1179/ also be used for models created by other means such as photo- 019713609804516992. The Artec scans were a little quicker.08. Adding a bespoke background and changing using an Ultimaker 2 3D printer with PLA filament. P. It is important for all museums to value their visitors.culher. the later part of the workflow (post-proces. Where possible the lighting and material properties to best display the models took specimens will be printed at life size. 2009. The University of Dundee like many Universities has a 3D Most models uploaded in under five minutes and could then be edited printing facility on site (DJCADMake). 40–45. Photogrammetry for 3D digitizing bones of museums in developing their own online collections. especially for this specific workflow. Bravin. 2016).H. Karas. 2016.CRPV.. meaning that this doesn’t have to be content for the project.1007/978-3-642-16873-4_29〉. C. taking closer to half and to share with us information regarding D′Arcy Thompson's original an hour to set up and scan. Conserv. 10..com/britishmuseum). Reischig. 1992. commercial. X.. meaning that it Medical Art visit the museum as part of their programme of study and could potentially be used by artists and non-artists alike. Cambridge. On Growth and Form.