Categories
biology imaging notes

The blastopore of bryozoan embryos

This is a bryozoan embryo exhibiting its blastopore. These animals are discreet but ubiquitous in oceans and lakes all over the world.

Bryozoan embryo during gastrulation revealing its blastopore.
Embryo of the bryozoan Membranipora membranacea under confocal microscopy.

What we see is the DNA inside the nucleus of the cells of the embryo. The color gradient indicates if the nuclei are closer (yellow) or further away (purple) from the microscope camera.

The embryonic cells are arranged in a circle and form a central opening that we call the blastopore. This opening, in bryozoans, will become the mouth of the animal after the embryo develops.

You can follow the process on video or learn more details in the paper.

What about our mouth, where does it come from?

Categories
articles code

Convert video to animated GIF

Something that I began doing more often is converting videos of developing embryos or marine invertebrates to animated GIFs. But how to do this conversion without affecting the quality of the video?

A jellyfish moving its tentacles. Source: Cifonauta.

Some time ago I found this guide to convert videos to high-quality animated GIFs using the tool FFmpeg. The trick is to generate a color palette based on the original video to improve the color quality of the GIF. Based on this guide I created a small bash script to make my life easier and perhaps yours too ;)

Check it in https://github.com/nelas/gif.sh

Categories
notes biology

Living entoprocts

Live footage of entoprocts! Tiny colonial invertebrates that capture food with a crown of ciliated tentacles

Categories
notes code

The PostdocNet logo

The PostdocNet is an organization that represents the collective of postdoctoral researchers working in the Max Planck institutes spread throughout Germany.

The network is relatively recent, only founded in 2019, but has already put forward important proposals to improve the working conditions and career development of postdocs.

A few months ago they contacted me to help re-design their logo and website to better represent the identity of the organization. Since I enjoy creating websites and I’m sympathetic to the mission (disclaimer: I’m a postdoc) – I accepted the challenge :)

After some rounds of feedback from the PostdocNet working groups, the final version of the logo is finally here:

The new PostdocNet logo.

You can read more about the story behind it here.

Now the website is next…

Categories
biology notes

Cifonauta’s 8th anniversary

Cifonauta, our image database for marine biology is 8 years old today! Almost 12k photos and videos annotated with species names, geolocation, habitat, life mode, microscopy technique and more.

Visit: http://cifonauta.cebimar.usp.br Follow: @cifonauta

Cifonauta 8th anniversary
Categories
biology imaging notes

Chubby ribbon worm

A chubby ribbon worm juvenile #Nemertean #WormWednesday

Chubby ribbon worm
Juvenile specimen of the nemertean Lineus ruber under wide field fluorescence microscopy. Magenta: Nuclei; Green: F-actin.

Categories
science notes

Fly Station

Fly Station is ready for the #LNdWDD @mpicbg

Fly station.
Categories
biology imaging notes

Larva of a lamp shell

Larva of a lamp shell, also known as brachiopod.
Terebratalia transversa (Sowerby, 1846)
Oil on canvas
167.95 µm × 167.95 µm
Categories
biology imaging notes

Fruit fly embryo under lightsheet microscopy

A short video that I made about the embryonic development of the likeable Drosophila, also known as fruit fly or vinegar fly, won an honorable mention in the Small World in Motion.

A single embryo imaged from four different angles.

The details on the techniques I used and the video on its full resolution are available for download and re-use on the Wikimedia Commons.

Categories
music articles

The Pluteus Trip

The Pluteus Trip is a music compilation that I created inspired by the life of these nifty echinoderm larvae named pluteus. It was released more than ten years ago in my (now defunct) music blog ccNeLaS.

The album is freely available at:

https://archive.org/details/ThePluteusTrip

Please find the original description below and enjoy the trip!

The Pluteus Trip front cover.
Front cover of The Pluteus Trip.

Plutei are born in the seawater. They represent a specific life stage (larva) of some marine invertebrates, the Echinoderms. Most of them are less than 1mm long, so tiny that inertial forces are dominated by viscous forces of the water.

Just imagine if air was honey and we had to go for a walk… Plutei can swim and feed in this environment using their long arms and cilia. However, Plutei are ephemeral. They swim (and eat) for weeks or maybe months, before something else takes place.

Currents can take them really far away from the place they were born. Millions of Plutei are born at once. How many would survive? How many would be thousands of miles away? How many would get proper food and not be eaten?

Plutei carry the tissue of adults inside them. The food they eat goes to adult tissues. In the end, the adult in formation takes over the larval body and the Pluteus is gone.

Plutei are part of the ocean’s hidden life. Organisms we can’t see easily, but that certainly got in between our toes when walking along the beach, or were swallowed during a swim…

The Pluteus Trip back cover.
Back cover of The Pluteus Trip with the song list.