Microscope Images Mouse Embryo Development at the Cellular Level

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Researchers at Howard Hughes Medical Institute’s Janelia Research Campus have developed a new microscope that uses adaptive light-sheet microscopy techniques to capture mouse embryo development at the single-cell level. The team is making the microscope, associated computational tools, and its imaging data freely and publicly available.

A new light sheet microscope has given scientists a window into mouse development. Courtesy of K. McDole et al/Cell 2018.
A new light-sheet microscope has given scientists a window into mouse development. Courtesy of K. McDole et al./Cell 2018.

The new microscope adapts itself to changes in size, shape, and optical properties of a mouse embryo post-implantation and captures the embryo’s development from gastrulation to early organogenesis at the cellular level. Using the microscope over a 48-hour window when rudimentary organs begin to take shape, scientists could follow every embryonic cell and pinpoint where it went, what genes it turned on, and what cells it met along the way. Researcher Philipp Keller said that the new microscope provides “literally a cellular-resolution building plan of the entire mouse.”

During the time period the researchers wanted to observe — from six and a half to eight and a half days after fertilization — a mouse embryo grows by more than an order of magnitude. This makes the embryo a moving target for the microscope, because it is continually changing size and position. Even a human camped out in the lab, adjusting the scope’s focus every five minutes for two days, couldn’t capture crisp images of the entire embryo, Keller said.

The new, smart microscope allows the researchers to image the progression of development in the mouse embryo by doing the work for them. At the center of the microscope, a clear, acrylic cube houses the embryo imaging chamber. Two light sheets illuminate the embryo, and two cameras record images, giving researchers a view of early organ development, including dynamic events, in high-resolution detail.

The microscope is equipped with a suite of algorithms that track the embryo’s position and size, map how the light sheet moves through the sample, and select the best images while keeping the embryo focused and centered in the field of view. Because the embryo is constantly changing, the microscope must constantly adapt, making decisions in milliseconds, over hundreds of images, at hundreds of different time points.

The researchers collected nearly a million images for each embryo examined. They then developed a computational framework for reconstructing long-term cell tracks, cell divisions, dynamic fate maps, and maps of tissue morphogenesis across the entire embryo. By jointly analyzing cellular dynamics in multiple embryos registered in space and time, they built a dynamic atlas of post-implantation mouse development. Without this computational toolkit, it would have taken a human two to three years to keep track of every cell, Keller said.

The Janelia team is providing the atlas of post-implantation mouse development together with the microscopy and computational methods it developed as a free resource to other scientists.

The research was published in Cell (

With the development of an adaptive, multi-view light-sheet microscope and a suite of computational tools, researchers have captured the first view of early organ development inside the mouse embryo. Courtesy of K. McDole et al/HHMI/Janelia Campus.

Published: October 2018
Research & TechnologyHoward Hughes Medical InstituteJanelia CampusAmericaseducationMicroscopylight sheet microscopyadaptive imagingcomputational image analysisLight SourcesOpticsImagingBiophotonicsmedicalBioScan

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