A Guide to Zebrafish Research - See More Details at a Glance

Communications, Corporate

June 26, 2025

A Guide to Zebrafish Research - See More Details at a Glance

Recognize fine structures and multiple colors in zebrafish during screening, even at low magnification, with Leica microscope solutions

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To obtain optimal results while doing zebrafish research, especially during screening, sorting, handling, and imaging, seeing the fine details and structures is important. They help researchers make the right decisions for the next steps. Known for outstanding optics and resolution, Leica stereo microscopes equipped with transmitted light bases and fluorescence illumination offer appropriate solutions for zebrafish imaging. High resolution, color fidelity, and optimal contrast enable researchers to make insightful decisions.

Basis for correct decisions when screening & sorting zebrafish

Do you struggle to see all pigments and fine structural differences in your zebrafish? The identification of the right phenotype is crucial and can be demanding.

See more details – Leica zebrafish screening solutions allow you to recognize fine structures and multiple colors even at low magnification. The acquired results can mean a clearer understanding of the zebrafish nervous system, heart, blood vessels, and pigmentation.

Improve your work experience by

Easy selection of an optimal contrast;
Having a homogenous contrast over the entire field of view (FOV);
Maintaining a steady contrast without re-adjusting over the entire zoom range.

Make a difference when screening & sorting zebrafish with Leica stereo microscopes.

Methanol-fixed zebrafish in glycerol. All structures of the developing organs can be seen. Sample courtesy: Mosimann Lab, University of Zürich, Switzerland. — Methanol-fixed zebrafish in glycerol where all structures of the developing organs can be seen. Courtesy of Mosimann Lab, University of Zürich, Switzerland.

Zebrafish Research Overview articles

Imaging and Analyzing Zebrafish, Medaka, and Xenopus

Transgenic zebrafish larva where fluorescent proteins label the heart muscle blue, blood and blood vessels red, and all circulatory system cells green. Image recorded with a M205 FA microscope.

Imaging of Cardiac Tissue Regeneration in Zebrafish

Image of a single slice taken from a zebrafish heart showing the ventricle with an injury in the lower area. Nuclei of all cells are indicated with blue, nuclei of the cardiomyocyte heart muscle cells with green, and the proliferating cells with red. Courtesy of Laura Peces-Barba Castaño, Max Planck Institute for Heart and Lung Research, Germany.

Using U-Shaped Glass Capillaries for Sample Mounting

Light sheet microscopy tilescan of zebrafish.

Reveal information with different contrast options

Cleary see the non-fluorescent stains in your zebrafish with brightfield stereo microscopy and the Leica transmitted light (TL) bases:

Evaluate staining and see the realistic colors of your zebrafish;
Investigate internal structures and visualize fine details with different contrast methods.

See how you can go from contrast to recognition with one-handed operation.

Fluorescence screening: Don’t let background noise mask your signals

Detecting xFP fusion proteins can be very challenging. The goal is to keep the expression of fluorescent proteins at low levels for realistic physiology. Signals are, therefore, faint and hard to identify.

In this case, your microscope setup should not be working against you with high levels of autofluorescence.

The Leica solution to this problem:

A separate excitation channel in fluorescence stereo microscopes, i.e., Triple Beam;
A specially designed mirror in light bases that helps prevent autofluorescence;
Adjustable flaps covering the automated light base to minimize autofluorescence during imaging.

The result is a clear fluorescence signal against a noise-free, black background.

Screening Fluorescent zebrafish: See weak signals against a black background. Image courtesy: Mosimann Lab, University of Zürich, Switzerland — Screening zebrafish where weak fluorescent signals are seen against a black background. Courtesy of Mosimann Lab, University of Zürich, Switzerland.

Handle your specimen with ease

Being able to easily see the orientation in 3D with Leica stereo microscopes ensures that you see exactly where your tools are. That way, you don’t accidently injure your zebrafish.

With Leica solutions, you can:

Handle zebrafish specimens easily with a good hand-eye-coordination;
Set injections and lesions precisely;
Optimally position your sample for imaging.

Hatching zebrafish 48hpf in Rottermann Contrast. Sample courtesy: Vermot Laboratory, IGBMC Strasbourg, France — Hatching zebrafish 48 hpf (hours post fertilization) viewed with Rottermann contrast. Courtesy of Vermot Laboratory, IGBMC Strasbourg, France.

Efficiently obtain publishable results

Functional imaging of zebrafish specimens is one of the most demanding tasks to perform in the laboratory. Researchers can achieve it by taking advantage of Leica automated stereo fluorescent microscopes.

Work with zebrafish more efficiently thanks to software-based control of:

Fluorescence excitation light, filters, and shutter;
Transmitted light contrast;
X/Y/Z positioning of specimen;
Microscope camera for image acquisition;
Magnification; and
Specimen environment.

With a fully automated Leica transmitted light bases, functional imaging of zebrafish is done more easily, as they provide the resolution and contrast required.