{"id":2185,"date":"2022-12-01T10:32:11","date_gmt":"2022-12-01T10:32:11","guid":{"rendered":"https:\/\/blogs.cardiff.ac.uk\/bioimaging\/?p=2185"},"modified":"2023-03-30T09:21:53","modified_gmt":"2023-03-30T09:21:53","slug":"in-focus-ar-palynology-probing-the-reality-of-nature-nature-of-reality","status":"publish","type":"post","link":"https:\/\/blogs.cardiff.ac.uk\/bioimaging\/in-focus-ar-palynology-probing-the-reality-of-nature-nature-of-reality\/","title":{"rendered":"IN FOCUS: AR Palynology: Probing the Reality of Nature\/Nature of Reality."},"content":{"rendered":"
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Above: Augmented reality visualisation of pollen grains 3D rendered in gigantic proportions. You wouldn’t want one of these getting stuck up your nose!<\/p><\/div>\n

Back in 2015 we developed some novel methodology that allowed us to generate 3D printed models from confocal z-stacks of microscopic samples.\u00a0 At the time, we showcased the technique by making 3D prints of pollen grains from various plant species for use in science education and outreach activities, musing that a physical, tangible model would allow improved 3D conceptualization of these microscopic structures \u2013 original blog article here<\/a>. The work generated a fair amount of interest and resulted in requests for 3D printed models of pollen grains from far and wide (e.g.,<\/em> the Smithsonian National Museum of Natural History in the US, the UK Met Office<\/a>, National Botanical Garden of Wales<\/a> etc<\/em>). Following publication<\/a> of our methodology in 2017 other researchers soon followed suit, creating their own 3D printed models from confocal datasets utilizing methods<\/span>\u00a0<\/span>similar to ours. By this time, we had turned our attention to virtual reality (VR) as a tool to experience\/manipulate microscopic objects, as well as larger <\/span>more complex biological models in virtual space – something we saw as a logical\u00a0 evolution of the 3D learning experience. You can read more about this in a <\/span>separate blog<\/a> and see the progress we made in developing the resource via a <\/span>short video<\/a> on our YouTube site.<\/span><\/p>\n

Fast-forward to present, a global pandemic, accelerating environmental change, and a cost-of-living crisis\u00a0 – the economic fallout from COVID, the folly of Brexit<\/a>, a war in Ukraine, and gross government incompetence.<\/a>\u00a0To borrow a quote from a certain Vladimir Ilyich Ulyanov, there are decades where nothing happens, and there are weeks where decades happen. Well, quite!<\/p>\n

But what of the 3D pollen models? Well, for one, <\/span>coronaphobia<\/a> has meant that people are less inclined these days to be handling and passing around shared resources such as plastic pollen models or VR headsets at risk of spreading\/contracting germs. Moreover, plastic is increasingly being <\/span>viewed negatively<\/a> due to the environmental damage caused by plastics and \u2018frivolous\u2019 3D printing could be seen as increasing the existing plastic problem<\/a>. Lastly, with the cost-of-living crisis\/looming recession, it would seem that no one can afford to do anything other than feed themselves and try to keep warm these days, let alone commission 3D pollen prints from the Bioimaging Hub – particularly since there’s now a growing number of pollen models available through 3D printing sites such as <\/span>Sketchfab<\/a> etc. And so, with these concerns in mind, we\u2019ve donned our thinking caps and come up with a plan to address the prevailing zeitgeist.<\/span><\/p>\n

Firstly, we\u2019ve decided to make our entire repository of 3D pollen models publicly available, free of charge, under a Creative Commons CC-NY-NC licence via the newly developed NIH3D website<\/a> (formerly the NIH3D print exchange) which is a leading\u00a0 community-driven portal for sharing and downloading\u00a0 bioscientific content for 3D printing and interactive 3D visualization<\/span>. Under the terms of our licence, the models can be used, shared, or modified for non-commercial purposes, as long as the creator(s) are properly credited. To date, we\u2019ve made available 3D models of seventy distinct species of pollen grains and spores through the Bioimaging Hub’s new NIH 3D profile page<\/a> which have now been curated into a special collection, the 3D Pollen Library<\/a> We have also included all source data (confocal z-stack files in Carl Zeiss Image .czi file format). To the best of our knowledge, this represents the largest single collection of 3D pollen files available online and the plan is to add more models plus supporting data in future<\/span>. For cross-referencing, relevant links have been included to major palynological databases, <\/span>PalDat<\/a>\u00a0and <\/span>the Global Pollen project,<\/a>\u00a0and, of course,\u00a0 Wikipedia – the fount of all knowledge : ) We\u2019ve also showcased a small selection of our pollen models on <\/span>the Bioimaging Hub’s Sketchfab site<\/a> \u2013 these can\u2019t be downloaded directly, however you can manipulate the models on screen and view them in VR \u2013 further information <\/span>here<\/a>.<\/span><\/p>\n

Secondly, we\u2019ve been experimenting with augmented reality (AR) as a tool to allow visualization and exploration of our 3D models in real-world environments. <\/span>The beauty of AR, of course, is that it doesn\u2019t require a headset,\u00a0 just a smartphone or tablet which are now more ubiquitous than ever<\/span>.\u00a0 Thus, a 3D model in the relevant file format\u00a0 (usually <\/span>\u00a0<\/span>.glb<\/em> or .gltf<\/em>) <\/span>can be downloaded directly to an individual’s smartphone or tablet and, using appropriate AR software, seamlessly integrated with real time digital information from the camera for display on the <\/span>touchscreen<\/span>. <\/span>This allows users to personally experience a real environment with generated perceptual information overlaid upon it. <\/span>Within the AR environment, the models can be scaled up or down, freely moved and rotated via the touchscreen, or circumnavigated and explored both externally and internally via directional information from the device’s sensors,<\/span>\u00a0<\/span>\u00e0 la\u00a0<\/span>Pokemon-GO<\/a>. <\/span>This allows for a\u00a0 highly realistic and immersive interactive experience (different from the artificial environments of VR) thus facilitating<\/span>\u00a03D conceptualization<\/span> of the embedded model. Furthermore, freed from the physical encumbrance of a VR headset, the user is less likely to blunder into office furniture, moving traffic etc or experience the nausea, headaches and dizziness of VR-associated cybersickness<\/a>.<\/span><\/p>\n

So how does one view our 3D pollen models in AR? Well, it\u2019s quite straightforward really, but to make things even easier I\u2019ve put together a set of<\/span>\u00a0<\/span>instructions (below) that should get you up and running in next to no time:<\/span><\/p>\n

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  1. Install a free AR app on your mobile device (smartphone or tablet) from the Google Play or Apple App stores that handles .glb<\/em> (GL transmission format binary) files \u2013 this is the common standard file format for AR\/VR visualisation. \u00a0There are quite a lot of AR apps to choose from and we\u2019ve only tested the NeoSpace AR app<\/a> on android devices but this seems to work quite well.<\/li>\n
  2. Go to the Bioimaging Hub\u2019s NIH 3D webpage \u2013 link here <\/a>– select a 3D pollen model, and then click on the DOWNLOAD <\/strong>option.<\/strong> You will then see a list of\u00a0 the files that we\u2019ve made available for download (refer to screenshot below). These include:<\/li>\n<\/ol>\n