notes science

Introduction to Science Mastodon

After a first try back in 2020, I’ve recently migrated my account to my new social handle (@bruvellu) and started using Mastodon again.

I’m excited about it. Migrating away from Twitter (and other corporate social silos) will be good for the web in general and for science communities in particular.

Here’s my introduction to the Science Mastodon community:

biology articles imaging

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.

notes biology

Mechanobiology conference

Mechanobiology investigates the role of physical forces in embryonic development. I’ll present my work on how the fold that divides the head from the trunk in Drosophila embryos—the cephalic furrow—may have an important mechanical role in gastrulation. The conference Mechanobiology in development and disease is happening in the EMBL Heidelberg.

notes biology

True Facts: Sea Stars

The latest True Facts about Sea Stars is unmissable. The video is filled with delightful echinoderm biology and even covers some recent discoveries on these enigmatic creatures. Watch it!


Moved to

Hi! I’m migrating from my old domain to To continue following the blog update the feed address to See you!

notes biology

The Spiral

The Spiral
The snail Littorina angulifera (photo by Alvaro E. Migotto). Cifonauta marine biology image database

Here’s a personal view about body symmetry and body openings from someone who lived through the evolution of bilateral symmetry.

Form? I didn’t have any; that is, I didn’t know I had one, or rather I didn’t know you could have one. I grew more or less on all sides, at random; if this is what you call radial symmetry, I suppose I had radial symmetry, but to tell you the truth I never paid any attention to it. Why should I have grown more on one side than on the other? I had no eyes, no head, no part of the body that was different from any other part; now I try to persuade myself that the two holes I had were a mouth and an anus, and that I therefore already had my bilateral symmetry, just like the trilobites and the rest of you, but in my memory I really can’t tell those holes apart, I passed stuff from whatever side I felt like, inside or outside was the same, differences and repugnances came along much later.

Excerpt from The Spiral, a tale in the delightful Cosmicomics collection of science-inspired short stories by Italo Calvino.
biology notes

Platynereis or Spotify?

Every time I open Spotify, I see the pattern of engrailed expression in an early Platynereis larva. Once you see it, there is no turning back!

Platynereis or Spotify?
The similarity between engrailed expression in Platynereis and the Spotify logo. A) Whole-mount in situ hybridization of engrailed in a 48h larva of the annelid Platynereis dumerilii (Prud’homme et al. 2003). B) Illustration of engrailed expression pattern in Platynereis. C) Spotify logo. D) Illustration of adapted Spotify logo.


Prud’homme, B., de Rosa, R., Arendt, D., Julien, J.-F., Pajaziti, R., Dorresteijn, A. W. C., Adoutte, A., Wittbrodt, J., & Balavoine, G. (2003). Arthropod-like expression patterns of engrailed and wingless in the annelid Platynereis dumerilii suggest a role in segment formation. Current Biology: CB, 13(21), 1876–1881.

science notes

UNESCO Recommendation on Open Science

UNESCO released a recommendation last year with the first international framework for open science policy and practice. This is something every researcher and institution should be aware of and strive for. Science is an amazing endeavor, but it can be more diverse, inclusive, and fairer.

The video nicely sums it all up.

The four pillars of open science

UNESCO OpenScience f2
  1. Open scientific knowledge (publications, research data, educational resources, software, hardware)
  2. Open science infrastructures (virtual or physical instruments, equipments, platforms, repositories)
  3. Open engagement of societal actors (crowdfunding, crowdsourcing, volunteering, citizen science)
  4. Open dialogue with other knowledge systems (indigenous peoples, marginalized scholars, local communities)

The definition of open science

For the purpose of this Recommendation, open science is defined as an inclusive construct that combines various movements and practices aiming to make multilingual scientific knowledge openly available, accessible and reusable for everyone, to increase scientific collaborations and sharing of information for the benefits of science and society, and to open the processes of scientific knowledge creation, evaluation and communication to societal actors beyond the traditional scientific community. It comprises all scientific disciplines and aspects of scholarly practices, including basic and applied sciences, natural and social sciences and the humanities, and it builds on the following key pillars: open scientific knowledge, open science infrastructures, science communication, open engagement of societal actors and open dialogue with other knowledge systems.

You can download and read the whole UNESCO Recommendation on Open Science at I first heard about it through the telescoper.

biology notes

The Great Divide

Cephalic furrow the early fold
Divides the embryo in one go.
Pulling in on its own
Deep it sinks into the yolk.

This great divide of tissue fold
Splits the embryo in back and front.
But why the furrow once it grows
Stretches flat and gone it goes?

A fold that folds and then unfolds
Leave us wondering what’s the role.

science notes

( Science ( Wonder ) Art )