Visualize Disease On The Microscopic Level With Molecular Flipbook's 3D Animations

Dr. Janet Iwasa's new app brings much-needed 3D animation technology into the ER.

Images & video courtesy of Dr. Janet Iwasa, Ph.D. 

One University of Utah Ph.D. is at the forefront of helping doctors see like artists, with a software that allows professionals in the field to fight disease in 3D. Her name is Dr. Janet Iwasa, and the technology behind these 3D molecular animations is called Molecular Flipbook, a huge innovation within the realm of medicine-focused illustration. Not only could Molecular Flipbook allow researchers to design better experiments, but the software's shallow learning curve encourages medical professionals to depcit what they're studying with more ease than ever before, especially as it's free and open-sourced.

A TED Fellow, Dr. Iwasa recently spoke at TED2014 to unveil her latest strides in visualization technology. Explore the technology in its finest below, as well as a Q&A with the doctor about why animation (and visualized hypotheses) are essential for improving how we understand and cure diseases.

Chromatin remodeling: ATPase from onemicron illustration on Vimeo.

The Creators Project: You work in a field in which highly technical lectures are routine. Did you adjust your talk for TED? Was this a departure from your typical lectures?

Janet Iwasa: The main difference between my TED talk and lectures that I have given to molecular biologists was the length. It's a challenge to be limited to only four minutes! In other (longer) lectures, I would often provide a lot of examples of animations I've worked on in the past, and talk about how these visualizations have played an important role in teaching and exploring hypotheses.

I might also provide some context about how I became an animator while working towards a Ph.D. in cell biology. And for non-biologists, I'd provide a bit of background about what raw data looks like, and why we can't just take a video of molecules carrying out these interesting processes in cells.

Molecular Flipbook can help us do just that, but instead of video, theyre 3D animations. It's pretty complicated stuff, but to the layperson, how does it work?

There are a lot of animation software packages out there, but nearly all of them were designed with Hollywood/the entertainment industry in mind. For my animation work, I primarily use Autodesk Maya. I learned how to use it during a 3-month full-time bootcamp-type training course, which was great, but was just about the absolute minimum necessary for me to start making my own animations.

I've tried teaching Maya to biologists, and what inevitably happens is that students forget how to perform simple tasks -- like rotating the camera -- if they haven't used the software for a week or two. I wanted to think about how to create an animation software that would be specifically designed for molecular biologists to create 3D animations of molecules.  

Could Molecular Flipbook be used to allow researchers to design better experiments? Could it be implemented to share research with a broader audience? 

The major goal was to create software that was intuitive, with a very shallow learning curve. The hope was that a researcher could work on an animation, then do some experiments for a few weeks or months, and be able to immediately pick up where they left off on the animation without having to relearn the software. Another major goal was to create an online database where researchers could share the source files (or scene files) for the animations, allowing different researchers to download the source files and change animations to reflect their own personal hypotheses. If they then uploaded their own animations and source files, you could start seeing how a hypothesis could evolve over time and vary between individuals.

entry draft from onemicron illustration on Vimeo.

I received a grant from the National Science Foundation for the project, and brought together a team of biologists and programmers to try and make Molecular Flipbook a reality. It's been a couple of years, and I'm thrilled with where we are so far. Our testing has shown that biologists are able to create a simple 3D molecular animation in five-to-ten minutes, after watching a five minute tutorial. Our database is currently in the works, but should be up and running later this spring.

Another thing that I'm proud of is that the software is open source and completely free. The database will be open to anyone to view and download animations and source files, and we hope the animations will make it out to other communities, such as the educational community, in addition to the research community.

Why are visualization technologies important? This is obviously a huge step forward from the "So what are we looking at now?" sort of poke-and-prod-style inquiry exposed in all those old, creepy medical portraits.

What I've found from dozens of collaborations over many years is that animation is a powerful means to explore an idea. In biochemistry and molecular biology, researchers are interested in understanding complex molecular interactions that may involve dozens of different molecules moving over space and time. The main (and usually only) way that researchers visualize their hypotheses, however, is with drawings that typically depict molecules as simple 2D shapes, perhaps connected by arrows to indicate movement. These are essentially stick-figure drawings of molecules.

These oversimplified illustrations only capture a small fraction of the information we have. Creating an animation—which I often think of as a visualized hypothesis—can be an extremely creative process, helping researchers realize, for example, if there might be something missing from their hypothesis.

Clathrin-mediated endocytosis from onemicron illustration on Vimeo.

How do you see Molecular Flipbook evolving in the future?

We've just released the beta version of Molecular Flipbook. In the short-term (by the summer), we're planning on adding a number of additional features that will benefit researchers seeking to create molecular models.  We're seeking feedback from our users for what types of features to think about for the future.  One thing that has already come up is the ability to create .stl files, to allow the models to be made into physical objects using a 3D printer, and also the ability to export animations into other file formats that can be read by other animation softwares.  

We're planning on seeking a new round of funding for future developments, since funding for this project will be ending this summer. One of the features we'd love to add is a cloud-based rendering engine for our users. It would be great to think about a "virtual cell" that dynamically incorporates the different molecular animations we have in our database. For example, perhaps the user could fly into the mitochondria, and see animations that were created by our users who specialize in mitochondrial biology. It could be a great way to learn!

Here at the Creators Project, we focus on the intersections between art and technology. In essence, Molecular Flipbook is a medium for doctors and scientists, in the same way Maya is a medium to the 3D animator. Could Molecular Flipbook ever be used to make art? 

Yes!  I'm happy to know that some of my work is appreciated as art by some, and I have been grateful for the opportunity to show some of my pieces in galleries and other public spaces. Similarly, I think it would be great if artists wanted to try using our software to create molecular animations, or if animations by researchers were appreciated for more than their scientific content. I know that I'm not alone in thinking that the molecular world is an incredible, intriguing and beautiful place, and would love to spread that idea through art.

Sounds like exactly what we're into! Lastly, let's talk animation: in terms of style I'm a bigger fan of Akira than Toy Story. Are you more the 2D or 3D animation type, and what's your favorite animated movie? 

I love animation, and I don't discriminate between 2D and 3D! For me, it's more about the story, and having characters that I can connect to. My favorite animated movies tend to be Miyazaki movies (Princess Mononoke, My Neighbor Totoro), and Pixar movies (WALL-E, Ratatouille, Up). When it comes to 3D animation, though, I know it can be kind of a pain to watch movies where you're constantly going, "Wow, that piece of cheese looks so real! Look at how the light hits it... I wonder how they textured that!" etc. 

Well, we're glad the opposite is true for the doctors hard at work using Molecular Flipbook. Thanks for speaking to us!

Desire to learn more about molecular biology? Learn about the foundations of life on Earth, through a series made on Molecular Flipbook: Exploring Life's Origins. And, while you're at it, check out more of Dr. Iwasa's revolutionizing work on her offiicial website, Onemicron