Cell Shorts | Bringing cell science resources to the classroom

July 12, 2019

undefinedHigh school students access freely available resources from the Allen Cell Explorer. Photo courtesy of Tom Martinez.

Ashley Ziemer loved high school biology. After finishing this year’s class, taught by Tom Martinez at Glenbard East High School in Lombard, Illinois, she says wants to major in biology in college.

“I just find it so amazing how everything is connected,” said Ziemer, describing what she just finished learning about cells in her junior year. “All the different parts have their different jobs to do to be functional.”

Teaching cell biology to high schoolers is not easy, Martinez said. But after 37 years of teaching, he’s got a few tricks up his sleeve. “I think this year we knocked cells out of the park,” he said.

For the past two years, part of their cell biology curriculum has included sifting through real images of cells using the 3D Cell Viewer, an online cell viewer that lets users investigate any of 40,000 different colorful 3D images of human stem cells collected by researchers at the Allen Institute for Cell Science, a division of the Allen Institute. The viewer is openly available on

Martinez learned about these publicly available images by chance through a talk given by Allen Institute for Cell Science Executive Director Rick Horwitz at a stem cell conference Martinez attended several years ago. He’s one of a handful of teachers who have stumbled across the Institute’s resources and incorporated them into their classrooms. But this month, Allen Institute researchers have debuted newly created educational materials — pairing posters with lesson plans about neuroscience and cell biology — aimed at augmenting biology classes for high school or college students.

Biology teachers like Martinez need real-life examples from the scientific world like this, he said, to dispel some misconceptions that well-meaning cell biology textbooks can generate.

“The students come in with preconceived ideas of what a cell is,” Martinez said. “They think cells are static. They have no idea how dynamic they really are.”

This year, the class also used the Visual Guide to Human Cells, an interactive 3D cell viewer, in their studies of cell division.

“The fact that it was 3D and I could see all the parts of it, that made it feel much more real,” said Megan High, a Glenbard East student who also took Martinez’s class this year.

“After all these years taking biology, it was so cool to finally be able to see what a cell looks like in our body,” Ziemer said. “We always see cells [in the textbooks] as these circles, perfect-looking, but they’re really these organic things that are completely unique to what they do.”

Preparing students for an automated world

undefinedImages of human induced pluripotent stem cells from the Allen Institute for Cell Science's 3D Cell Viewer

Carlos Goller, Ph.D., wants to make sure his molecular biology college and graduate students at North Carolina State University are ready for the modern scientific world when they graduate — and that means preparing them to deal with cutting-edge automated technologies.

“Don’t fear the robot; the robot will help you do experiments,” Goller quipped. “Students start to shut off when they see spreadsheets full of data that come out of these technologies, and they really should be able to tackle that. To get there we have to make this a common part of our curricula.”

Being comfortable with high-throughput biology means not just understanding the individual techniques, but also how to parse and analyze the large amounts of data they generate, Goller said.

In addition to teaching biotechnology courses at NCSU, Goller leads a National Science Foundation-funded network along with Dr. Sabrina Robertson of the University of North Carolina at Chapel Hill. The network, HITS, aims to develop and share educational case studies or lesson plans focused on high-throughput science, or science that involves large amounts of automatically generated data. Goller used images and models from to generate a case study. The students work through the study to screen cell images to determine whether a drug has a specific effect on a structure known as the endoplasmic reticulum in human cells.

The real-life examples from the Allen Institute image databases fit into this exercise, Goller said, because they show cells’ variation in structural size and shape — an important concept for any scientist-in-training who is trying to sift out an abnormal effect, for example, due to a specific drug, from normal variability.

'Real cell biology is kind of messy’

Eric Shelden, Ph.D., an associate professor of biology at Washington State University, wanted to recreate for his college students his own early experiences studying cells. During graduate school, Shelden studied microtubules, which are part of the cell’s internal scaffolding and form intricate highways inside the cell.

“The first time I saw cells stained to reveal microtubules, it reminded me of fireworks,” Shelden said. “It’s like the fourth of July every time I look at those images. I was captivated by that.”

At WSU, he both teaches large cell biology classes and leads a research team. He’d love to have all his students experience that same captivating feeling, but with more than 100 students in some of his classes, there’s no feasible way to bring them all into the lab for hands-on learning, he said. So he was looking for the next-best way to emulate this type of research experience.

Shelden saw a talk at WSU by Horwitz that also showcased the 3D Cell Viewer and the Institute’s collection of cell images.

“I’ve long had this idea of having cells under a microscope streamed to a web browser,” Shelden said. “The Allen Institute’s cell images are pretty close to that. There are these massive amounts of data that are accessible to anyone through the internet. It got the wheels turning to think about how I could incorporate this into the classroom.”

Together with his WSU colleague Erika Offerdahl, Ph.D., and Allen Institute for Cell Science visualization expert Graham Johnson, Ph.D., Shelden developed a “virtual laboratory” for his students to study cell division through the Allen Institute’s large collection of cell images. Shelden wrote a program that assigns 20 random cell colony images from the Allen Institute database; each image contains about 30 cells. The students have to find and count cells that were captured in different stages of cell division in their unique collection of images and then plot the data to show how many cells they find in each stage. The three recently published their virtual laboratory lesson plan for other college classrooms to use in the journal CourseSource.

The exercise was not easy, Shelden said, but those students who finished told him they learned a lot — and not just the nitty gritty about cell division, but about scientific research in general. The stages of cell division are nowhere near as easy to pick out in real images as in textbook illustrations.

“This gives them an appreciation for how powerful cell science can be, but also how difficult it can be,” Shelden said. “This is real life, as opposed to what you see in the sterile cartoon versions in the textbook. Real cell biology is kind of messy.”

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