Prof Cynthia Whitchurchi3 Institute, UTS
Erin GloagPhD Student, i3 Institute UTS
Dr Lynne TurnbullMicrobial Imaging Facilityi3 Institute UTS
Ben SimonsData Visualisation
The goal of this research project was to improve understanding of how bacteria coordinate their activities as large populations of individual entities. The reason the researchers were interested in this behaviour is because bacteria tend to live as communities, not individually. By gaining a better understanding of these activities, the researchers hope to come up with better ways of preventing and treating infections.
Research has revealed that the rules bacteria use to coordinate their own multi-cellular behaviours are very similar to the rules that higher organisms use to coordinate group behaviours. This is important because many bacteria use this behaviour to be able to migrate across surfaces to actually spread infections.
If we can understand how the bacteria are coordinating their behaviours, maybe we can actually then impose our own will on the bacteria so that we can then stop that behaviour. This is really important because we’re entering a global crisis of antibiotic resistance, and it’s really imperative that we understand how bacteria cause infection, and by understanding the basics of how they do that, we may be able to come up with new ideas as to how to prevent and treat infections, either by creating new antibiotics, or preferably even by using non-antibiotic approaches.
The Data Arena provided the researchers with a powerful visual tool to be able to interact with their data. We were able to develop a pipeline to import the research data into the Data Arena. This allowed the researchers to examine, in greater detail, the quantitative behaviour of the cells. Visualisation of this data within the Data Arena proved to be a very powerful means of gaining an increased understanding of how the bacteria can coordinate together and act as a cohesive entity.
The microbial imaging facility within the UTS Faculty of Science has access to a very high-end microscope called the “super-resolution” microscope. The Data Arena developers have been working on a pipeline for users of the microscope to be able to bring their data into the Data Arena in a simple way. The high resolution visualisation environment of the Data Arena will allow these users to gain greater insights into their data sets than would be possible when viewing the images on a normal sized computer screen.
The Data Arena allows users to view images of bacteria and parasites that are smaller than the width of a single hair as interactive 3D visualisations that may be viewed in high definition and scaled up in size to the dimensions of a human being!
Here's a new word for you - Stigmergy! It's an idea, coined in 1959 by French biologist Pierre-Paul Grassé -- we all follow trails. At all world scales, from the largest thing to the smallest you can imagine: there are trails.
Generally speaking, when we walk through a forest, we don't cut our own path. We follow one made before us. At our scale there's roads and paths and corridors. At larger scales, container ships find their way through a harbour following marker buoys. Aeroplanes follow flight paths. Even planets orbit the sun on an elliptical path. At small scales, ant colonies exhibit stigmergic behaviour. They follow a complex network of trails marked by pheromones.
At the microscopic scale, researchers at UTS have shown bacteria also signal and exhibit stigmergy. Through the microscope we see paths and traffic-jams and co-operative behaviour.
The movie on the right is in Top-Bottom Stereoscopic Format. In the Data Arena, when wearing a pair of Stereoscopic Active Shutter Glasses synchronised to the video projectors, you see this movie in 3D Stereo. Parts of the movie stand out from the screen, parts fall in behind the screen. You feel like you can reach out and touch it.
Active Shutter glasses simply contain see-through LCD glass which momentarily go completely black so they cannot be seen-through. It blanks so quickly, hopefully you don't notice. The glasses are set to block the left-eye, then the right-eye, then the left again and so on. Synchronised to the video display, when the left eye is "open" the video projector shows the top image for the left eye. This is during the short moment when the right eye is completely blocked by the Glasses' LCD. Then the glasses & projector switch to show the image for the right eye.
All the video projectors swap together, in sync with all the glasses (each person in the Data Arena wears these glasses). We can still see each other & yet experience 3D Stereo. Switch fast enough (30 fps per eye) and the result is each eye sees a slightly different image (top or bottom), there's no flicker, and the effect is 3D Stereoscopic. The image, in this case Bacteria, appears to be floating in 3D space, in full 360-degrees surround.
The Data Arena prefers stereo movies in Top/Bottom format. This one was 1920x2400 pixels.