Clarafi

What do you like the most about this field?

It ticks the boxes for me – it fulfills the lyrical, creative side of my nature and the didactic, analytical one as well. It’s also very rewarding when you observe how your animations are connecting the dots for the observer and that they are gaining an understanding of the subject they might not have had if they were reading a written explanation or trying to make sense of 2D images.

How and where did you acquire your current skillset in scientific visualization? Was it all via a graduate or other program or are you self taught? If so, did you use any particular online resources to help with your training?

After my Eureka moment with Drew, I was lucky to be able to work part time at my sales job and undertake a year long course in Multimedia. This gave me enough material to put together a portfolio to be accepted into the Graduate Certificate 3D Animation course at the Australian Film Television and Radio School. After that I set about working on my own projects, such as animating my PhD (a really great idea suggested by Drew), doing a bit of freelance work and entering the odd competition. I also did all the online tutorials on Molecular Movies, the precursor site to Clarafi. This really helped get my skill base up and create my first showreel. I was then incredibly lucky to be offered a two year mentorship as part of the Vizbi Plus project with Drew Berry, at the Walter and Eliza Hall Institute of Medical Research, Melbourne. This was where I learnt most of what I know now!

How do you feel your PhD training has an impact on your scientific visualization work? What specific skills from your PhD training have empowered you in your scientific visualization work? Do you think your PhD training has given you a unique perspective on viewing, interpreting, and creating scientific visualizations?

For me Biomedical Animation is all about problem solving and how you’re going to make the objects on your screen interact and tell a story. Contrary to popular belief, there is no magic ‘make cell divide button’. Similarly, a PhD is primarily about problem solving and how you design and conduct your experiments to test your hypotheses. The way I carry out research for my animations is also directly influenced by my PhD and is similarly rigorous. When conducting scientific research you follow a systematic set of guidelines outlining your questions and how you approach them. I follow a similar systematic approach when creating an animation and it’s always roughly the same ie research, literature review, storyboard, script, modeling and animation, lighting and cameras, rendering, compositing, sound effects and narration, with a lot of to and fro in the production stage. I guess I look for this formality in others’ work as I feel it results in a clear and concise story.

Can you provide a specific example/situation of where you think your PhD training changed the way you designed something, interacted with someone or navigated a situation?

One thing my PhD taught me is that there are many ways to approach a specific question and obtain an answer, some better than others. It’s a matter of determining the best approach for the task at hand, and of course, therein lies the art! It’s exactly the same with animation. Eric Keller put it very succinctly when he said something along the lines of ‘There are a million ways to achieve something with Maya and only 500,000 of them are wrong.’

In my latest animation about tetanus, I had to illustrate how the firing of the motor neurons controls the release of acetyl choline, which in turn controls skeletal muscle contraction. This was achieved using expressions, allowing a top-down approach, where one set of commands controls all others. This avoids key framing each individual action to give greatest flexibility and control, so that changes can be made easily with minimal effort.

What do you consider some of the biggest barriers to entering the field? Are they technical, training, scientific, professional (availability of jobs or projects)?

I feel the biggest barriers to the field in Australia are probably training and professional. There are no formal scientific/biomedical animation courses available here and you have to make do with entertainment industry offerings, which of course are useful, but you need to be able to adapt them to suit. There are, however, many online resources available, if you have the motivation to learn on your own. Molecular Movies, Clarafi and Plural Sight to name a few. There are also few employment opportunities for this kind of work in Australia and you would generally end up freelancing or needing to convince the various scientific research institutions of their need for an in-house animator. Everyone can see the value of what we do here, but unfortunately it’s still considered an ‘icing on the cake’ kind of enterprise. This attitude is changing though, so don’t let it put you off.

Which practitioners (or what visualizations) have been most inspirational to you?

I have been incredibly lucky to train under Drew Berry and both he and Etsuko Uno have been instrumental in my development as an animator. I also greatly admire Gael McGill and the team at Digizyme, particularly for providing the wonderful resource that is Clarafi, opening up the world of scientific visualisation for beginner and professional alike. I also regularly look at the work of design houses such as In Vivo, Radius, Hybrid and Nymus 3D for creative inspiration. In terms of fine art, I love the private, introspective worlds created by Vermeer and the holistic approach of the Secessionist artists such as Gustav Klimt and Egon Schiele, who saw the importance of painting, sculpture and architecture in their movement. Someone I think really inhabits the intersection between fine art and science is David Goodsell. His watercolours of the myriad molecules found in the cell interior and cell membrane are stunning.

Which conferences would you recommend to those interested in this field and why? What particular insights or benefits did you get out of attending this (these) conferences?

Thus far, I’ve only had the chance to attend one conference and that was Vizbi. Although there were few practicing animators present, the breadth and depth of knowledge was truly phenomenal, giving you a taste of the possibilities and inspiring you to think outside your own little realm. I enjoyed it immensely. A particular highlight was the presentation by Jane Richardson, who developed the universally accepted method of representing protein ribbon structures that we take for granted. I’d also love to get along to SIGGRAPH one of these days.

If there was one resource, tool or conference that you could wish for to facilitate your work, what would it be?

I seem to be terrible at simulating depth of field and end up faking it with blurs in After Effects. A simple fool proof way of doing this would be most welcome.

What other advice would you offer those interested in either a professional or full-time academic career in scientific visualization?

Take the plunge. It is incredibly creative and rewarding. Do all the tutorials on Molecular Movies to give you grounding in 3D animation and then try animating a subject close to your heart, such as your Masters or PhD, if you went down that road. It really helps if you animate a subject you know inside and out to begin with. Try to get together a portfolio of work to show to a potential employer, where you can receive further training or to gain access to a formal animation course, if you decide that route is for you. Talk to other people in the field to ask their advice on how they entered the field and also be brave enough to ask their opinion of your work. I found most professionals, such as Drew, really giving of their time and expertise.

Please comment briefly on the samples/links that you have submitted for this profile… why in particular are you proud of these and what do you hope viewers will notice and get from seeing them?

Sample 1: Insulin receptors spanning the cell membrane
I was very pleased to be involved with this project, as it helped to explain the pioneering work of Dr Mike Lawrence’s lab (WEHI) into determining the structure of the insulin receptor and just how insulin binds in the receptor binding pocket. I hope that viewers will notice the purple insulin molecule docked into the receptors. I am proud of the complex rig I created that enabled conformational changes in the receptor to allow signal transduction, with simultaneous movement of the individual protein domains and also atomic motion.

Sample 2: Ciliated airway epithelium with mucus trapping foreign particles
This was the first time I used nHair systems in Maya, to create animated cilia that mimicked epithelial cilia motion, although greatly slowed down. I was pleased with the way the cilia was actually able to move the mucus layer lying on top, brushing it away and thereby removing the foreign objects trapped in it, including pollen, dust and bacteria. I would like to think the viewer can sense the brushing motion of the cilia.

This animation was officially selected for the Raw Science Film Festival 2016. It also won an Award of Exceptional Merit for Environmental/Health PSA and Viewer Impact: Content/Message Delivery categories and an Award of Excellence for SFX Animation at the Doctors Without Borders Film Festival 2017. This animation also won the Warren Sturgis Motion Media Award at BioImages 2017.

Sample 3: Tetanus toxin arriving in the cell body of motor neurons, located in the spinal cord
Strongly influenced by the anatomical drawings of the central nervous system by Ramon y Cajal, this image illustrates tetanus toxin (orange) arriving in the motor neuron cell bodies, where it then interferes with control of motor neuron firing. I am proud of the level of detail I achieved with this shot, hopefully giving a sense of the tangled network of neuronal connections, some neurons firing (teal glow), whilst others are at rest. I used expressions to control firing, so that the animation is semi-automated, avoiding individual key frames.

Where do you think the field of scientific visualization is ‘going’? Do you perceive any trends in its evolution or are there certain directions that you would like to see implemented?

Currently in vogue is visualisation and making sense of massive data sets. First there was the data generated by the human genome project and now there is all the protein sequence data generated as a result of selection of interesting candidate genes. I got to see a lot of this at the recent Vizbi conference and it was fascinating stuff. It’s intriguing to me that all this ‘making sense’ also looks appealing; with order and understanding comes beauty.

There is also a strong trend towards virtual and augmented reality and truly immersing yourself in the biological world. John McGhee is doing great things with actual patient data, allowing the patient to take a virtual tour into their own stroke affected brain or cardiac infarct, in the hope this positively influences patient outcome.

And then let’s end with a simple question… What is your ‘10 year plan’ in terms of what you hope to accomplish in scientific visualization?!

I’m not much of a one for long term planning and tend to follow the most interesting path that presents itself. After all, if you haven’t achieved your 5 or 10 year plan, does this mean you’ve failed? I don’t think so. My motto is more along the lines of ‘If opportunity knocks, open the door’, even though that may mean deviating from your planned pathway.

In terms of things I would like to try, I am really keen to move into VR for educational purposes, to inspire an engagement with the sciences in school students. I am also really keen to try using actual biological simulation data in an animation to demonstrate realistic motion, rather than faking an approximation of it. Ultimately, I hope to work in an academic environment, collaborating with scientists in their research and finally making the outcomes of that research accessible to the general public. Many people are frightened of science, both the ideas and the language. I wish to remove this fear through the use of visual, 3D representations, rather than abstract concepts. The ultimate aim of my work is to help people appreciate the beauty and drama of biology.

Portfolio Link: https://vimeo.com/majadivjak