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Fluorescent-labeled cells used to train neural networks. Image: Allen Institute

New 3D models of living human cells generated by machine-learning algorithms are allowing scientists to understand the structure and organization of a cell's components from simple microscope images.

Why it matters: The tool developed by the Allen Institute for Cell Science could be used to better understand how cancer and other diseases affect cells or how a cell develops and its structure changes — important information for regenerative medicine.

"Each cells has billions of molecules that, fortunately for us, are organized into dozens of structures and compartments that serve specialized functions that help cells operate," says Allen Institute's Graham Johnson, who helped develop the new model.

What they did: The researchers used gene editing to label the nucleus, mitochondria and other structures inside live human induced pluripotent stem cells (iPSC) with fluorescent tags and took tens of thousands of images of the cells.

  1. They then used those images to train a type of neural network known as Generative Adversarial Networks (GANs). That yielded a model that can predict the most likely shape of the structures and where they are in cells based on just the cell's plasma membrane and nucleus.
  2. Using a different algorithm, they created a model that can take an image of a cell that hasn't been fluorescent-labeled — in which it's difficult to distinguish the cell's components ("it looks like static on an old TV set," Graham Johnson says) — and find the structures.

What they found: When they compare the predicted image to actual labeled ones, the Allen Institute researchers said they are nearly indistinguishable.

The advance: Gene editing and fluorescent dyes often used to study cells only allow a few components to be visualized at once and can be toxic, limiting how long researchers can observe a cell.

Plus, "knowledge gained from more expensive techniques or ones that take a while to do and do well can be inexpensively applied to everyone’s data," says the Allen Institute's Greg Johnson, who also worked on the tool. "This provides an opportunity to democratize science."

Go deeper

Updated 5 hours ago - Politics & Policy

Coronavirus dashboard

Illustration: Annelise Capossela/Axios

  1. Health: CDC director defends agency's response to pandemic — CDC warns highly transmissible coronavirus variant could become dominant in U.S. in March.
  2. Politics: Biden readies massive shifts in policy for his first days in office.
  3. Vaccine: Fauci: 100 million doses in 100 days is "absolutely" doable.
  4. Economy: Unemployment filings explode again.
  5. Tech: Kids' screen time sees a big increase.
  6. World: WHO team arrives in China to investigate pandemic origins.
Dave Lawler, author of World
6 hours ago - World

Alexey Navalny detained after landing back in Moscow

Navalny and his wife shortly before he was detained. Photo: Kirill Kudryavtsev/AFP via Getty

Russian opposition leader Alexey Navalny was detained upon his return to Moscow on Sunday, which came five months after he was poisoned with the nerve agent Novichok. He returned despite being warned that he would be arrested.

The latest: Navalny was stopped at a customs checkpoint and led away alone by officers. He appeared to hug his wife goodbye, and his spokesman reports that his lawyer was not allowed to accompany him.

Mike Allen, author of AM
8 hours ago - Politics & Policy

Biden's "overwhelming force" doctrine

President-elect Biden arrives to introduce his science team in Wilmington yesterday. Photo: Kevin Lamarque/Reuters

President-elect Biden has ordered up a shock-and-awe campaign for his first days in office to signal, as dramatically as possible, the radical shift coming to America and global affairs, his advisers tell us. 

The plan, Part 1 ... Biden, as detailed in a "First Ten Days" memo from incoming chief of staff Ron Klain, plans to unleash executive orders, federal powers and speeches to shift to a stark, national plan for "100 million shots" in three months.

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