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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?

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notes software

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
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
notes science

Interview for the Portrait of Science

Recently, I had the honour to be interviewed for the Portrait of Science. It’s a beautiful project created by Magdalena Gonciarz to get to know the people who do science (aka the scientists). Check out the project’s Tumblr and Facebook pages!

Categories
biology imaging notes

A beautiful nemertean

The ribbon worm Tubulanus #WormWednesday #Nemertea

The nemertean Tubulanus.
Adult specimen of the nemertean Tubulanus annulatus collected in Norway.
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biology notes

Understanding the evolution of cleavage patterns in early embryonic development

Video summary about our work on bryozoan development and the evolution of cleavage patterns published in BMC Biology!

The video was produced by Research Square. Also available on Vimeo.

Categories
biology notes

Bryozoan cell lineage

What happens when cleavage patterns evolve? Some insights from bryozoan embryonic development: https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0371-9

Summary bryozoan cell lineage
Categories
biology imaging notes

Bryozoan embryos viewed from the animal and vegetal poles

The first 24 hours in 1.5 minutes of bryozoan embryos.

Categories
biology imaging notes

Bryozoan embryos viewed from the animal pole