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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

State Department to set up new cyber bureau to combat hack attacks

Secretary of State Tony Blinken speaks on the challenges during an October conference in Quito, Ecuador. Photo:y Felipe Stanley/Agencia Press South/Getty Images

Secretary of State Tony Blinken announced Monday plans for the State Department to create a new bureau of cyberspace and digital policy.

Why it matters: The establishment of the bureau and plans for a new envoy to oversee critical and emerging technology come after a series significant hack attacks and other online crimes, notably ransomware assaults on U.S. infrastructure.

Biden rejects Trump's latest executive privilege claims

Photo: Jim Watson and Saul Loeb/AFP via Getty Images

The White House on Monday rejected two more of former President Trump's claims of executive privilege over documents that the House select committee investigating the Jan. 6 Capitol riot requested, CNN first reported.

Why it matters: Trump's legal team is seeking to block some of the panel's requests for records by invoking executive privilege, which can allow presidents and their aides to sidestep congressional scrutiny. The Biden administration has maintained that it will evaluate on a case-by-case basis.

Amazon warehouse workers in New York file petition to hold unionization vote

Amazon workers and their supporters rally outside the National Labor Relations Board's regional office in Brooklyn, New York City, after filing a petition requesting an election to form a union. Photo: Gabby Jones/Bloomberg via Getty Images

Amazon warehouse workers in New York City filed a petition on Monday with the National Labor Relations Board (NLRB) to hold a vote on unionization.

Why it matters: The move comes six months after an organizing effort was defeated at Amazon's distribution center in Alabama.

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