Under the Microscope – Visualizing Blood Vessels in the Brain of Zebrafish

Dr Elisabeth Kugler | Director of Zeeks – Art for Geeks Ltd | Twitter @Zeeks_art
| Instagram @zeeks.artforgeeks | Facebook Zeeks – Art for Geeks


Yes, zebrafish. The ones you can buy in the pet shop!

Zebrafish are important models in biomedical science to answer fundamental questions of body development, health, and disease. A lot of work is focused on understanding how tissues and organs develop, because once we understand how something is formed, it is easier to understand how it is maintained in health and how it is breaking down in disease. 

While adult zebrafish are about 2-3 centimetres in size (which is the length of a matchstick), when studying developmental processes many labs examine zebrafish embryos (smaller than the tip of a matchstick). Thus, we need microscopy to elucidate and reveal the hidden microscopic worlds. 

A picture containing text

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Image shows the blood vessels of a 4-day old zebrafish embryo in blue and the respective brightfield image underneath. Two views, lateral and dorsal, are shown for reference. Embryo head width is about 600 micrometer. Image c/o Dr Elisabeth Kug

The microscope

While the size of the embryos seems very small, in microscopic terms this is actually very large and we normally only study tissues in the scale of a few micrometers rather than hundreds of them. This poses a challenge as light interacts with matter [1]. To address this, light-sheet microscopy (LSFM) has become the ideal solution to acquire data in large tissue samples.

In a nutshell, LSFM uses a sheet of light to illuminate a thin optical section of a sample and the data are acquired by an uncoupled emission detection objective. This means, that while in conventional confocal microscopy, a whole cone of light shines through the sample, in LSFM it is a thin plane that is illuminated and this whole plane is imaged at once. Together, this results in less photobleaching, fast acquisition, and large fields-of-view [2]. 

Chart, funnel chart

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Image shows simple LSFM setup with the uncoupling of the illumination and emission/detection objective. Image c/o Dr Elisabeth Kugler.
A close-up of a human brain

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Image shows shows the blood vessels in the brain of a 3-day old zebrafish visualized with two vascular markers (magenta and green). These vessels are about 10 micrometer in diameter which is approximately the thickness of a spider silk strand. Image c/o Dr Elisabeth Kugler.

The science art

As the acquired data are rather large in microscopy terms, this means that there is a lot of data to work with for analytical purposes, but also to endeavour on data examination paths for science art. Dr Elisabeth Kugler (Twitter @KuglerElisabeth) has used her microscopy data in the last few years to share her scientific passion using visual science art [3].

More recently, Elisabeth has formed the company Zeeks – Art for Geeks Ltd, which is all about data. This will allow her to focus on all things data and explore new avenues how to communicate scientific research using science art. 

Screenshot of a section of Dr Elisabeth Kugler’s science art image gallery.This shows how colourful and artistically beautiful data can be. Image c/o Dr Elisabeth Kugler.


[1] E. Kugler and E. Reynaud, “LSFM series – Surfing on the data freak wave! Part II: Before imaging: Know your sample (geometry),” FocalPlane, Oct. 10, 2020. https://focalplane.biologists.com/2020/10/10/lsfm-series-surfing-on-the-data-freak-wave-part-ii-before-imaging-know-your-sample-geometry/ (accessed Nov. 16, 2022).

[2] J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, and E. H. K. Stelzer, “Optical sectioning deep inside live embryos by selective plane illumination microscopy,” Science, vol. 305, no. 5686, pp. 1007–1009, Aug. 2004, doi: 10.1126/science.1100035.

[3] the Node, “SciArt profiles: Elisabeth Kugler,” the Node, Jul. 28, 2021. https://thenode.biologists.com/sciart-profiles-elisabeth-kugler/science-art/ (accessed Nov. 16, 2022).

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