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Compared to the low-tech way of studying development in mice — scrutinizing day-old mouse fetuses, then another bunch that are an hour older, and more that are two hours older, and so on up to the end of gestation at 20 days or so — a new microscope has a lot to recommend it. And not just because there aren’t enough mice (or graduate students) in the world to see embryonic development by this snapshot-in-time approach.

The “laser light sheet microscope” can peer inside living mouse embryos, capturing the first-ever real-time images of organ development inside a mammal, scientists at the Howard Hughes Medical Institute’s Janelia Research Campus in Virginia reported in Cell on Thursday.


The nearly 1 million images per embryo show the earliest heart cells beginning to beat, the gut taking shape, and other mouse-making cellular dances never seen before, revealing the biological choreography that turns an early embryo into one with its organs in place.

Despite studying embryogenesis in mice and other lab animals for centuries, scientists “still hardly know how cells migrate, how they organize during the formation of tissues, and how they interact with their neighbors,” said Janelia’s Philipp Keller, who led the invention of the microscope and the software that runs it. With that microscope, he said, “for the first time we were able to follow single cells across the entire developing embryo.”

Mouse embryos are notoriously hard to image. Light damages them. They don’t stay still. Keeping them outside the womb for more than 12 or so hours kills them. So the Janelia team had to first make a little acrylic cube, filled with nutrients and other necessities of life, to sustain mouse embryos removed from the womb. Then they had to make their microscope “smart,” able to adapt, millisecond by millisecond, to keep the moving, growing embryo and its migrating cells in focus.


The embryos could be kept alive for only two days, so Keller and his colleagues chose a key window of time within that limit: the 48 hours from when the embryos were 6.5 days old. That’s the period from when they develop three distinct cell layers (as human embryos also do) through early organ formation.

During those two days, the embryo grows more than tenfold, to about 3 millimeters across (the length of a ladybug). Even anchored at one point in a pool of nutrients, it “drifts around like a little balloon,” said developmental biologist Kate McDole, lead author of the paper.

To capture the changes by brute force would require adjusting the focus of an ordinary confocal microscope every five minutes, and even then parts of the embryo would often be blurry or outright invisible.

Instead, the scientists aimed sheets of laser light at the embryo in the cube, revealing cells at every depth. Two cameras recorded images. Software tracked the embryo’s position and size, adjusting the light sheets as often as every few milliseconds to produce the clearest, most detailed images. Additional software allowed the cameras to follow tens of thousands of embryonic cells and track where they went and what cells they met along the way, eventually creating video of the whole process. (The Janelia team is making the microscope, computational tools, and imaging data publicly available for free.)

When the foregut forms, the team could see that “it’s not this slow, gentle process,” McDole said, but a biological big bang: “The whole thing just caves in and makes a huge hole.” And the neural tube, which later forms the brain and spinal cord, knits together like a zipper, stretching across the embryo. Watching organs form, she added, “was just very cool.”