New Tool Allows View of Cell Division in 3D Models

The Allen Institute for Cell Science recently launched the Integrated Mitotic Stem Cell, a new tool that visualizes mitosis. Mitosis is cell division in the typical human stem cell. It’s how a cell splits into two, duplicating all its genetic information and cellular components.

The Integrated Mitotic Stem Cell merges images of 15 separate cellular components, creating a 3-dimensional map of what a human cell looks like during different steps in cell division. The idea is that it can assist researchers in better understanding how the separate stages and different components of the cell work together—it’s also visually beautiful and entertaining, which makes it a valuable educational tool.

“The biggest visualization consideration is helping people understand the three-dimensional relationships of structures relative to one another,” Graham Johnson, the director of the Animated Cell team at the Allen Institute, told Forbes.

Johnson’s group used several different lighting techniques, developing some of their own. Forbes notes that one challenge was the use of colors. If there are too many, it can make it difficult to interpret the images.

Johnson chose to stick to a coloring scheme where organelles with similar functions have similar colors, that are just different enough that you can distinguish them.

"These are color families that I thought hard about 20 years ago when I illustrated a textbook in cell biology," Johnson told Forbes. "Some of them were adopted in other books and other presentations over the years, so I’ve stuck with that standards."

Although there are applications for researchers, the images are an educational tool as well. Johnson pointed out, for example, that mitochondria presented in textbooks typically look like “stripy beans,” but that’s not a completely accurate visualization. “Even though a subset of biologists have known for decades that it’s a big network of interacting tubes, the visualizations that were created early on created entire generations of people who had an incorrect mental model about the shape of mitochondria,” he says.

The mission of the Allen Institute is to develop dynamic and multi-scale visual models of cell organization, dynamics and activities “that capture experimental observation, theory and prediction to understand and predict cellular behavior in its normal, regenerative, and pathological contexts.” The Allen Institute was founded in 2014 with a contribution from Paul G. Allen, who co-founded Microsoft with Bill Gates in 1975. Allen passed away on October 15, 2018.

Earlier this year, the Allen Institute launched a virtual reality headset to play its latest app, which allows the wearer to wander inside a simulated, circular room that has “targets” on the surrounding walls. The institute describes it, saying, “Several 3D, watermelon-sized human cells fall from the sky and land at your feet, jostling gently to find their place on the ground. In the VR game, users learn the different stages of cell division, or mitosis, by picking up the cells and pitching them at the correctly labeled target on the wall.”

The game is currently a part of the regular rotation of VR experience in the Pacific Science Center’s What is Reality exhibit. The Allen Institute didn’t start out targeting children when they developed it but were approached by educators who wanted to use it in the classroom.

The institute notes, “Even biologists can learn something from the game. The research team did some internal user testing with other Allen Institute scientists before the app was ready to debut at the [2018 American Society for Cell Biology meeting], and it was clear that not everyone knew what the stages of cell division look like in realistic, data-driven models.”

The institute hopes to build more complex VR apps, including building apps that will immerse the user in the world of a real 3D human cell that highlights significant structures that can be explored and manipulated to address specific goals.