PhD student Harish Mandalika develops 3D visualisation software

For his PhD program, Harish Mandalika is collaborating with MARS Bioimaging, Ltd to develop advanced tools for interacting with data. Specifically, he is going beyond the mouse and keyboard to give medical professionals a novel, intuitive way to study volumetric data from CT scans.

If you were to fracture a bone, radiologists would use a CT scanner to examine the break. Most CT scanners operate in black-and-white, and they generate flat 2D images. The MARS group has developed a proprietary color scanner that generates color 2D data, and using cutting-edge technology from zSpace, Harish has developed software that transforms these 2D scans into 3D images. (For more information about the MARS scanner, read this article from Idealog.)

Harish came to the HIT Lab NZ in 2013 because he wanted to study computer graphics. “Based on my skill set, that gives me two options: computer games and medical imaging,” he explains.

For Harish, working on medical imaging technology gives him motivation to work and publish research. “You can’t do a PhD for the sake of doing a PhD. You have to find something you truly care about, because you will have to push yourself when no one else will push you,” he says.

“If games weren’t that cool, people would still be playing them. But if medical imaging were better, it could save someone’s life,” he says.

At the HIT Lab NZ, he works alongside Dr Niels de Ruiter and Dr Alex Chernoglazov. He also works with Dr Phil Butler and Dr Anthony Butler, the father-son team behind the MARS group. Niels reconstructs the colour 2D images from the raw scans, and Alex works on creating visual models from the 3D information from the MARS scanner (a process called rendering).

Currently, the MARS scanner only fits small samples such as small animals or pieces of tissue, but the team is working on scaling it up to allow full-body scans of humans.

The zSpace monitor uses passive stereo technology to display 3D images. The monitors interacts with a pair of special glasses that track head motion. Since the zSpace interface unifies the physical and the virtual world, Harish describes it as mixed reality.

While developing the software, Harish consulted with a senior radiologist at the University of Otago Christchurch School of Medicine. He then conducted user studies with registrars and medical students to test whether having 3D zSpace images helped them diagnose fractured bones faster or more accurately — or whether it was just more fun!

For Harish, one of the most challenging aspects of this project has been writing the software. To make software that is compatible with the MARS scanner, he first had to  make his own rendering engine. This alone took more than a year to develop. Additionally, since zSpace is a small company, Harish had to either work around bugs and missing features, or fix them himself.

With the zSpace software and hardware, Harish can visualise tissue from small animals and humans. “Now, my software is like PR for the MARS group — it’s just cool,” he laughs.

Harish completed his Bachelor’s degree in Information Technology from India. He later completed his Master’s degree in Advanced Computing Science at the University of East Anglia in Norwich, United Kingdom, where he developed a software for real-time 3D volume drilling using the CUDA architecture. Before coming to the HIT Lab NZ, Harish worked as an intern in computer graphics at NVIDIA in London for one year.

Publications

Aamir, R., A. Chernoglazov, C. J. Bateman, A. P. H. Butler, P. H. Butler, N. G. Anderson, S. T. Bell et al. “MARS spectral molecular imaging of lamb tissue: data collection and image analysis.” Journal of Instrumentation 9, no. 02 (2014): P02005.

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