Developing A Digital Embryo.pdf

The European Molecular Biology Laboratory (EMBL) scientists, led by Philipp Keller, Annette Schmidt, and Jochen Wittbrodt, developed a technique to obtain a 3D representation of the first 24 hours of a zebrafish embryo's development. They refined the principles of single-plane illumination microscopy (SPIM) to create digital scanned laser light sheet fluorescent microscopy (DSLM). This technique allows for high imaging speed and image quality, enabling the tracking of cells dividing and moving in a developing embryo.

To record the development of a zebrafish embryo, the scientists took snapshots at very short intervals, typically every 60 or 90 seconds, over a 24-hour period. This resulted in around 400,000 images per embryo. The next challenge was to analyze the vast amount of data generated, which was solved by using clusters of computers working in parallel.

Each computer was given one snapshot of the embryo and told to look for cellular nuclei in that image. By combining the information for all slices, the scientists generated a digital embryo: a visual representation of all the embryo's cells, where they are at a given point in time, where they move to next, and when and where they divide. The result is a 3D time-lapse video of the developing embryo.

This enabled the scientists to shed new light on different stages of the embryonic development of zebrafish. At a very early stage, the zebrafish embryo is basically a group of cells sitting on top of the yolk sac. The cells divide in a wave that moves across the embryo, and the timing and molecular mechanism of gastrulation differ between organisms.

The scientists used a genetic strain of zebrafish, which is a genetically uniform group of animals used in laboratory experiments. They obtained a 3D representation of the embryo's development by scanning the embryo from one viewpoint, rotating it by 180°, and scanning it again. This allowed them to compose a full 3D image of the embryo.

The EMBL scientists "sliced" their zebrafish embryos every 60 or 90 seconds over a 24-hour period, obtaining around 400,000 images per embryo. They used clusters of computers working in parallel to analyze the vast amount of data generated. Each computer was given one snapshot of the embryo and told to look for cellular nuclei in that image. By combining the information for all slices, the scientists generated a digital embryo: a visual representation of all the embryo's cells, where they are at a given point in time, where they move to next, and when and where they divide.

The result is a 3D time-lapse video of the developing embryo. This enabled the scientists to shed new light on different stages of the embryonic development of zebrafish. At a very early stage, the zebrafish embryo is basically a group of cells sitting on top of the yolk sac. The cells divide in a wave that moves across the embryo, and the timing and molecular mechanism of gastrulation differ between organisms.

The scientists used a genetic strain of zebrafish, which is a genetically uniform group of animals used in laboratory experiments. They obtained a 3D representation of the embryo's development by scanning the embryo from one viewpoint, rotating it by 180°, and scanning it again. This allowed them to compose a full 3D image of the embryo.