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Mitotic waves and gastrulation in a fly embryo

Last year I published a snapshot of a mitotic wave in a fruit fly embryo. Here’s the video of that same embryo going through cleavage (nuclei divisions) and gastrulation (cell movements):

Mitotic waves (cycles of nuclei divisions) and gastrulation in the fruit fly Drosophila melanogaster. Also on Wikimedia Commons.

Mitotic waves

What you see at the beginning of the movie are the cycles of synchronous nuclei divisions. They happen in waves from the posterior to the anterior side (from right to left). Fly embryos undergo fourteen cleavage cycles after fertilization, but the movie only starts on the tenth. After each cycle, the embryo gets more packed with nuclei until they cover its entire surface.

Foe and Odell 1989 Nuclear cycles
Cycles of nuclear divisions in early Drosophila embryogenesis (Foe and Odell 1989).

At this point, the embryo is still a syncytium, that is, a single cell with many nuclei (yeah, that’s how flies do it). But on the 14th division cycle, about 11s into the movie, the embryo cellularizes, each nuclei being encapsulated by cell membranes. It’s a curious process, though not visible in this video.


Once cells form, the embryo begins to gastrulate. Gastrulation in flies is complicated, and many events happen at the same time. Cells move, invaginate, disappear, flow around the embryo, and start dividing again, again, and again. This movie shows about 3 hours of development, but embryogenesis continues for 24 hours post-fertilization until the embryo hatches out of the egg as a larva.

Foe and Odell 1989 Gastrulation
Developmental events during the gastrulation of Drosophila (Foe and Odell 1989).


The fly in the video is a transgenic line containing two types of fluorescent proteins. One is a green fluorescent protein (GFP) which is attached to a histone (H2A), a protein that binds to DNA in the cell nucleus. The other is a variant red fluorescent protein known as mCherry, which is fused to a protein that attaches to cell membranes (GAP43). In this way, we can see where the chromatin and cell membranes are located in the embryo during development (and learn something from it).


After collecting embryos, I glued them sideways on a tiny glass coverslip attached to the sample holder of the microscope, a Zeiss Z.1 Lightsheet. The scope has lasers to excite the fluorescent proteins which in turn emit light at different wavelengths. Filters allow us to capture the individual signals simultaneously. This is crucial for fast acquisition and makes two-color time-lapses possible.

I set the microscope to acquire 30 slices spaced by 3 µm, from the outer surface of the left side to the middle section of the body. One timepoint was taken every 35 s.


After the recording, I performed some image processing steps using Fiji/ImageJ. While 3D renderings for this type of data look great, I decided to flatten the image to 2D.

First, I ran Despeckle to reduce some noise (it’s low but helps smoothen the image). Second, I ran Subtract background... (with rolling=20) to remove out-of-focus information. Fly embryos have a dense yolk sac inside that can blur the fluorescence. Finally, I did a maximum intensity projection using the Z Project... command. This looks through the 30 slices in each pixel position, and only keeps the maxima values. It’s a practical way to visualize 3D data in 2D.

Lastly, we can color-code each fluorescent marker differently for better visualization. Some colors fit well together, others don’t. To map pixel intensities to color gradients in ImageJ we use lookup tables (or LUTs). Here, I chose a purple-yellow gradient named mpl-inferno for the DNA signal, a perceptually uniform colormap I like a lot, and a standard grayscale for the membranes (gray is great).

The end

That’s it, I hope you enjoy the video! I’ve uploaded a copy to Wikimedia Commons for eternity. Feel free to use it and if you need additional info, please contact me.

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