Categories
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!

Categories
notes

Moved to brunovellutini.com

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

Categories
notes biology

The Spiral

The Spiral
The snail Littorina angulifera (photo by Alvaro E. Migotto). Cifonauta marine biology image database http://cifonauta.cebimar.usp.br/media/9396/

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.
Categories
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
Source: https://unesdoc.unesco.org/ark:/48223/pf0000378841
  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 unesdoc.unesco.org/ark:/48223/pf0000378841. I first heard about it through the telescoper.

Categories
science notes

( Science ( Wonder ) Art )

Categories
notes biology imaging

Brachiopod larva in the Nikon Small World 2021

This image of a brachiopod larva was selected in the Nikon Small World 2021 photomicrography competition!

screenshot 20210918 094027 brave1441489128638992960
Categories
imaging biology notes

A mitotic wave

A mitotic wave traveling through an early #Drosophila #embryo #FlyFriday

3D HisGap cleavage cover
Early syncytial embryo of the fly Drosophila melanogaster. Nuclei (blue) are dividing in a wave from posterior to anterior. Membrane components (white) are already organized around the nuclei. The image is a frame from a timelapse acquired under lightsheet microscopy and rendered in 3D.
Categories
imaging articles code

ImageJ macro to synchronize and combine image stacks

The embryos I study rarely develop in perfect synchrony. That means that when I film them under the microscope some embryos will be younger—or older—than others.

ImageJ macro with Drosophila embryo
Using an ImageJ macro to help me analyze movies of Drosophila embryos.

For this reason, I often need to synchronize the recordings to make sure they all begin at the same embryonic stage. When the movies are synchronized I can combine them side-by-side, and it becomes much easier to compare and spot differences between two embryos.

ImageJ macros save time

Combining movies in Fiji/ImageJ is straightforward using the Combine... command. But synchronizing is way harder. It depends on human classification and involves some calculations and stack juggling that can (and will) become tedious.

To help me out, I wrote a small ImageJ macro available here: SyncAndCombineStacks.ijm. Follow below to see how it works.

Combined movies without syncing

That’s what unsynchronized movies look like. I combined them fresh off the microscope without any synchronization:

Two embryos of the fruit fly Drosophila melanogaster. Both were acquired in the same microscopy session. The top embryo is older than the bottom embryo.

Combined movies after syncing

Here are the same two movies now synchronized by the embryonic stage:

The same two embryos are now synchronized.

How it works

The macro performs the hard work. It calculates how many frames to trim from each stack. Then it duplicates the selected range of frames common to both stacks. Finally, it combines the synchronized recordings into a single image stack. All you need to do is to select the corresponding frames between the two stacks.

Step-by-step instructions

Here are the instructions step-by-step:

  1. Open both image stacks in ImageJ.
  2. Adjust the contrast if needed (before running the macro).
  3. Select a reference frame in the top stack (e.g. stage easy to recognize).
  4. Select the correspondent frame in the bottom stack.
  5. Run the macro and fill in the dialog parameters.
  6. Click OK, wait a few seconds, and check if the synchronization is good. Otherwise, re-run with different parameters.

Screencast

I’ve also recorded a small screencast:

Note! The macro does not touch the original stacks, but it outputs an RGB Color stack. There are a couple of reasons for that. Converting to RGB avoids contrast issues when the stacks have different pixel intensities. It also prevents quirks in video players that can’t handle 16-bit movies. But if you need to perform image analyses on the final stack, remove this option. I may add a checkbox for that in the future.

Categories
notes code

The PostdocNet website

Sometime ago I created a new logo for the PostdocNet, the network of postdocs of the Max Planck Society. The next step was re-designing their website… but then came 2020!

PostdocNet website
The new landing page for http://www.postdocnet.mpg.de/

Despite the challenging year, the website recently went live! I hope people enjoy the new visuals and I’m happy to have contributed to the PostdocNet :)

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?