Friday Feature: The Virtual Fish

Your Friday treat is a movie from Sean Megason’s lab of the development of a zebrafish ear.  Sean has a plan to provide a complete (“in toto”) image set describing the entire development of a vertebrate, using methods described here (Megason SG (2009). In toto imaging of embryogenesis with confocal time-lapse microscopy. Methods in molecular biology (Clifton, N.J.), 546, 317-32 PMID: 19378112).  When the project is complete — which will not be tomorrow — there will be a movie recording every cell division, and every morphological rearrangement, that happens as a zebrafish egg turns into a functioning fish.  And then you will be able to sit at your computer and analyze vertebrate development without needing to get so much as a single finger wet.

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This is from a zebrafish embryo in which both the nucleus (green) and the membrane (red) of every cell has been fluorescently labeled.  If you watch carefully, you can see individual cells divide (one green blob becomes two) and move into new positions, creating (for example) the circle of cells that then opens up into the tube of the inner ear.

Amazing.

But what is more amazing is that this is just one slice through a four-dimensional movie.  Cells that disappear from this plane are still present in the image set, and if you want to know where they went, you just need to slice the data a different way.

To obtain the movie, the embryo is placed on a slide that has a little fish-shaped dimple in it, to keep it in place as it develops, and imaged over the whole course of development (about 2-3 days). The mounting is key: you need the embryo to stay healthy as it develops, and you need it to stay as still as possible.  Next, you need to capture the images.  Using modern laser-scanning confocal microscopes, it’s possible to focus the light from the laser at a specific depth within the embryo (the z-plane) so that you can capture optical “slices”, or sections, of what’s happening within the embryo.  The embryo itself is not being sliced — it remains a whole, healthy and happily developing embryo.  You’re just taking a picture of what’s happening a few microns inside it.

Taking optical sections 1 μm apart, and scanning through the whole embryo every 2 minutes or so, will (eventually) give you a complete “four-dimensional” data set (all three dimensions of the embryo, plus time as the fourth dimension) that will make it possible to reconstruct every single cell division and cell movement throughout the whole volume of the embryo, as the egg develops into a fish. Once you have this image set, you can create your “virtual” fish.

Image acquisition and management is a huge challenge here; the Megason lab has developed an image acquisition tool called MegaCapture that automates acquisition.  [I do hope that they copyrighted that name before Dreamworks started working on MegaMind.  Can’t you just see MegaMind’s MegaCapture ray in the toy stores?  I also have a slight fear that if the movie is popular enough they’ll start working on a sequel.  Son of MegaMind; MegaSon, right?  And then nobody will ever be able to find the Megason lab via Google ever again.]

You can see the whole process and some of the results in this YouTube video, which also serves as a Megason lab manifesto:

All the software developed for this project is freely available on the Megason Lab Wiki, should you wish to try this at home.

Megason SG (2009). In toto imaging of embryogenesis with confocal time-lapse microscopy. Methods in molecular biology (Clifton, N.J.), 546, 317-32 PMID: 19378112