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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. 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.

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.

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

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

And here are the same two movies now synchronized by embryonic stage:

The same two embryos, now synchronized.

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. Here are the instructions step-by-step:

  1. Open both image stacks in ImageJ.
  2. Adjust 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.

I’ve 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?

Categories
notes 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.