NEWS

Biomedical Communications Alumni Association

UNIVERSITY OF TORONTO

Stuart Jantzen is an incredible animator and educator. He is the creator of Biocinematics, an educational science channel hosted on YouTube that uses animations to explore and explain topics in human biology. Before setting up Biocinematics, Stuart worked as a 3D Biomedical Technical Artist at AXS Studio, a medical animation studio in Toronto. He has also worked as a researcher with Jodie Jenkinson (University of Toronto Mississauga) and Gaël McGill (Harvard Medical School) as part of The Science Visualization Lab, investigating visualization in science by looking at attention cueing in molecular animation (https://sciencevis.ca/). With previous work as a bioinformatician, and an undergrad degree in molecular biology, Stuart brings a wide range of expertise and passion to his work.



Find his beautiful work at:

http://www.biocinematics.com/

https://www.youtube.com/biocinematics

https://www.instagram.com/biocinematics/


I understand that you worked as a bioinformatician before applying to BMC. How did you get into that line of work? What were some of the learning moments and challenges from that experience?


The adage "It's not who you know, it's who knows you" was true in this instance. I'd worked for a summer during my undergraduate degree doing DNA extractions. After I graduated, the professor running the lab was looking for someone to help with bioinformatics. He knew I had some interest in computer science in addition to my molecular biology degree, and offered me a job. Starting out, I knew very little about the necessary tools and techniques, most notably Python (a programming language popular in bioinformatics), so I learned a lot on the job. It was a tough learning curve, but I think there are two key skills (among many) that I've brought with me to all my animation work. The first is the ability to think like a programmer, which is not about knowing strange languages, but more about breaking down tasks or creative challenges into a logical sequence of smaller steps. The second, related to the first, is strategic troubleshooting: how to systematically investigate something that's broken until you find what's gone wrong.



How did you decide to pursue a masters in biomedical communication?


I've always loved making (and watching) animations, from flipbooks and HyperCard in elementary school, to claymation and Flash in high school, to 3D animation with Maya in my undergrad years. However, it wasn't until my time working in bioinformatics that I discovered the niche field of visualizing molecular biology through computer animation. Being inspired by the likes of Drew Berry, Eric Keller, and the "In Silico" authors (Jason Sharpe, Charles Lumsden, and Nicholas Woolridge), it didn't take me long (yet longer than it should have) to discover and apply for the MScBMC program.



Your master’s thesis, Recording the Illuminated Neuron: Functionality and in vivo applications of a new microprobe, explains and investigates how a microprobe can record information about neuronal activity. The animation component of the project can be viewed here. The Unity web app component is no longer supported.


Can you talk a bit about your process with your master’s thesis?


My master's thesis evolved quite a bit over the course of pre-production. It was conceived as an animation, which, given my history and interests was the natural medium. However, it became clear that an interactive component would fit well with the subject matter, i.e. how a new neuron microprobe works. The hybrid project ultimately became an animation to explain the functionality of the probe, and a Unity web app that allows users to locate and record neuronal activity. Because I had some prior experience with both 3D animation and programming, it wasn't as daunting an undertaking as it might otherwise seem, and I felt like I left BMC with a broad suite of skills.



How would you compare working with Jodie Jenkinson and Gaël McGill (within The Science Visualization Lab) as an associate researcher, to working on a master's thesis as a graduate student?


Research tends to take a much more convoluted path than a typical Biomedical Communications master's thesis. In the latter, overall there's a fairly linear progression from understanding the content and developing the learning objectives, to designing and executing the project. Yes, the scope can change and there's lots of decisions to make and iterate on, but the tried-and-true sequence of actions really assist in getting the whole thing completed in a year. With the research in the Science Vis Lab, I found there was a lot of exploration, new ideas, dead ends, and unexpected study results that directed us down new paths. I think this flow is closer to how most research happens, and is definitely not a bad thing. When exploring unanswered questions, you don't know where new discoveries will take you.



How did you come to conduct research on the specific topic of attention cueing in molecular animation while working as part of the Science Visualization Lab? What were some major challenges in this research?


Jodie and Gaël had already started researching this topic, and I joined the Science Vis lab to help develop the animations and conduct the studies with undergraduate biology students. In part, we were interested in understanding how best to convey the inherent randomness of molecular activity, but it quickly became clear how difficult it was for us to tease apart students’ pre-existing conceptions of cells and molecules. Until we grapple with the confusion and misconceptions that exist (and these are diverse), it's hard to address these in animations. We ended up doing a large-scale online "personalized quiz" to try to characterize how students think about how molecules move and interact, which it turns out is not an easy thing to assess.



How has what you learned doing this research carried through your work since, particularly the animations you’ve done for your YouTube channel, Biocinematics?


One thing that stuck with me was that our depictions of cell-scapes and molecules can imply realities we may not intend. In other words, some people interpret illustrations and animations as real captured images, or close to that: "Are those the real colours?", "Do they really move like that?", "Is the cytoplasm that sparsely populated?". Since we can never be entirely true to reality, in my YouTube animations I've made an effort to explain more how my videos are "illustrations" and why different representations are being used. Those clarifications are still not easy to convey, but I think it's worth considering.




Have you seen any recent medical/non-medical work that has been inspiring for you?


The watercolor work of David Goodsell has been inspiring me lately. He brings a clarity and simplicity to subjects of incredible complexity that is both paradoxical and beautiful. I also recently played an indie video game called Gris that appears to combine watercolor and hand-drawn animation to provide a mesmerizing, immersive experience. It really captured me. I've been thinking about NPR (non-photorealistic rendering) styles lately, so it was intriguing from that point of view.



I understand that you developed multiple pipelines for the medical animation workflow during your time as a 3D Biomedical Technical Artist at AXS Studio. Can you talk a little bit about this, and has this been an important element in your now independent animation workflow?


Part of my role at AXS was to help develop tools and workflows for the animation team and studio as a whole. I helped manage the render farm using Deadline, which I still use even as a solo animator on one computer. I created some tools to automate the setup of animation projects, and other tools to help with making various effects. Another effort was setting up and managing a database of the many visual assets produced by the studio. All of these automation and organization efforts are useful in helping me decide what systems and tools I might develop for my own work. Obviously constructing rigorous pipelines is more beneficial to larger teams, but I still find myself programming snippets and creating templates to speed up my workflow.




How did you go about taking on challenges within the workflow of creating videos for your YouTube channel, and having to take on new skills in order to do so?


After almost a decade of primarily Maya and After Effects, I've migrated to Houdini for animation and Blackmagic Design Fusion for compositing, which have fairly steep learning curves. However the overall sequence of steps (research, script, storyboard, models, animation, effects, rendering, compositing etc.) isn't too different from a BMC or studio animation. What I've found more of a challenge is the branding, self-promotion, and social media side of things. I suppose the other major challenge is managing my time and projects to have consistent, timely output. No one is safe from scope-creep.



How do you usually think of ideas for your YouTube videos?


While I'm not trying to create a comprehensive curriculum, I have a rough plan for covering biochemistry and molecular biology topics that I personally think everyone should know something about. I also try to discuss a subject in the context of an interesting question or relatable experience that hopefully makes it engaging for a general audience. For example, "Are You Really a Carbon Based Life Form?" introduces people to elements, atoms, and molecules. Other times I'll just have a question I'm personally curious about or don't fully understand, and will consider how to answer it through animation. I always try to make sure the topic relies on the visualization to convey an idea; in other words, hopefully viewers get a much deeper understanding of the material by watching, rather than by just listening to the narration.



Where do you think the future of animated/online education content is going?


That's a great question. I really don't know. I do think teachers are using more video and online content every year, but I also think that there's not a huge amount of consistently high quality educational animation available for life sciences. That's not to say there isn't some, but it's hard to know how much is getting into classrooms; sometimes there are cost or technology limitations. And animation resources are expensive and time-consuming to produce. I don't know that there's an obvious sustainable business model, but it's something I'd like to continue exploring.


BMCAA would like to express its thanks to Stuart Jantzen for taking the time to answer these questions and share his experiences in medical animation and research. Check out Stuart’s incredible work at http://www.biocinematics.com/.






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