Blog Post

Using Sketchfab as a public engagement platform for 3D models of biological structures

Craig Daly • Nov 08, 2019

And now, the gallery...

Research scientists at universities are under increasing pressure from funding councils and charities to provide evidence of both the impact of their research and their level of public engagement. Fortunately, internet based services and social media provide a perfect platform for such activities if used correctly. YouTube has become the premier vehicle for distribution of videos and animations of research findings. This vast repository has also become an essential learning platform for everyone with internet access.

A less well known resource is Sketchfab, a repository of 3D models that can be viewed on any device, and in Virtual Reality (VR) with embedded animations. The 3D objects (assets) can be viewed, downloaded or purchased for animation building, as game assets or 3D printing. The access rights are determined by the model owner – not Sketchfab. Several major museums and universities are now using Sketchfab to display their ‘exhibits’.

Glasgow Life Sciences

Glasgow Life Sciences (GLS) is a new public engagement and BioAnimation service within the School of Life Sciences at the University of Glasgow. The purpose of the service is to collect and curate the best of the College of Medical and Veterinary & Life Sciences’ (CMVLS) 3D datasets and process them for inclusion in the GLS Sketchfab collection, which can be viewed here:

https://sketchfab.com/GLS


At the time of writing (early Oct 2019) GLS has collected contributions from 13 different researchers within CMVLS and we hope to collect many more. The ability to view models in VR using either a mobile device or fully immersive headset creates a unique learning opportunity for students grappling with the complex 3D nature of many biological structures. The structure-function relationship in most (if not all) biological structures can be difficult to teach effectively and therefore learn.

Technology and Art

Datasets are collected from users in their native/raw format (typically as a series of TIFF images). GLS post processing techniques involve thresholding, segmentation, mesh reduction and refinement, animation, texturing and lighting. The best of the collection will feature in a fully immersive VR art gallery that is nearing completion and will be released in late 2019. The Sketchfab collection and VR Gallery will be demonstrated at Pharmacology 2019 (the annual winter meeting of the British Pharmacological Society) which will be held in Edinburgh this year (15-17th December).

To view any of the GLS models in 3D simply browse to the address ( https://sketchfab.com/GLS ). To view in VR you will need a Google cardboard viewer and smartphone as a minimum device. Click on the ‘view in VR’ icon found in the bottom right corner of the model (3rd icon from the right). If your PC or laptop is connected to a fully immersive headset the model should work automatically. We have found Firefox to be a more stable browser for VR viewing. One of the most recent additions is a beautiful reconstruction of the Islet of Langerhans comprising several pancreatic beta cells containing insulin granules. The cell nuclei are also shown. The model was provided pre-constructed by Fiona McCulloch (Medical Visualisation Masters student) and Prof. Gwyn Gould.


Previously, 3D models such as the one shown above and the sheep embryo from the collection would have been used once in an animation and never reused. The GLS collection provides a permanent public place for these models and our plan is to use these in both undergraduate and postgraduate teaching. We also hope that other universities may use the datasets in their own teaching.

Some of the models have already been used in the construction of 3D animations for teaching. These can be viewed at the author’s website and YouTube channel (links below):

https://www.cardiovascular.org

https://www.youtube.com/channel/UCz9GxddKUj2qrUmNgIpCrFg


References

Further details can be found in;

Daly, C. J. (2019) From confocal microscope to virtual reality and computer games; technical and educational considerations. Infocus Magazine, 54, pp. 51-59.

Daly, C. J. (2019) Examining vascular structure and function using confocal microscopy and 3D imaging techniques. In: Rea, P. M. (ed.) Biomedical Visualisation. Series: Advances in experimental medicine and biology (1120). Springer: Cham, pp. 97-106. ISBN 9783030060695 (doi:10.1007/978-3-030-06070-1_8)

Daly, C. J. (2019) Imaging the vascular wall: from microscope to virtual reality. In: Touyz, R. M. and Delles, C. (eds.) Textbook of Vascular Medicine. Springer: Cham, pp. 59-66. ISBN 9783030164805 (doi:10.1007/978-3-030-16481-2_6)

Daly, C. J. (2018) The future of education? Using 3D animation and virtual reality in teaching physiology. Physiology News, 111(Summer), p. 43


Author Biography
Craig DalyMSc PhD SFHEAis a Senior Lecturer in the School of Life Sciences, University of Glasgow (UofG), and has been involved in cardiovascular research, at UofG, for over 35years. Recently Craig's role has become more teaching focused, leading to a Senior Fellowship of the Higher Education Academy. For 25 years Craig studied adrenergic pharmacology using confocal microscopes, fluorescent ligands and 3D image analysis to investigate receptor distribution in the vascular wall. More recently, Craig has been using and repurposing his archive of 3D confocal datasets to create animations and virtual reality environments for teaching physiology and pharmacology.

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Risk Assessment and Insurance There are several examples online of Risk Assessments (RAs) for various purposes and contexts; I began with looking at the STEM Ambassador resources and followed links from there. The first step to producing an RA for a Science Club is to actually decide just what experiments you want to do (witness the fun I had researching this!). Making the decision I found was perhaps the hardest part, more so than the actual paperwork. However once I had a clear list, I adapted an online template to produce a grid, starting with the list of experiment titles on the left. Opposite each, I detailed the possible hazards; location; who might be affected; the risk rating; control measures; and finally the risk rating after these measures are taken. I also included for clarity an appendix showing how the risk is calculated. This can all be quite time-consuming; but once produced, your own template/draft can then be adapted/updated as required. I was able to complete mine while on the train down to London for the Pharmacology 2018 conference, which was a most satisfying and very productive use of the journey time (possibly more so than if I had been in the office….)! If running a Science Club, Public Liability Insurance is a good idea; it is not a legal requirement (unlike Employer Liability Insurance), but many organisations can request it or even insist on it, and it makes absolute sense to just have this from the beginning even if it is not required officially. Some companies do not offer Public Liability Insurance for a Science Club and refer you on to a more specialised broker so leave plenty of time to shop around, particularly as there can be quite a bit of to-ing and fro-ing with underwriters before giving a quote. Timing and Logistics How many children there are (can you set upper or lower limits?); ages/stages; whether people work in pairs, groups or individually; whether you have any assistance....how best to allocate/divide up equipment; what's the optimum number of set-ups to provide; are there occasions where a demo would be better; how many eyes in the back of your head you have...these all require careful consideration. And be prepared to revise as you go. It goes without saying that planning is absolutely essential, but don't be afraid to completely change or adapt procedures. It could be argued that for a successful well-run Science Club, organisation is just as important as the science (perhaps even more so). The Bare Bones So there it is; the Anatomy of a Science Club. To be continued…or evolved….!
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