Model Organisms in Research

A model organism is a species used by researchers to study specific biological processes. They have similar genetic characteristics to humans and are commonly used in research areas such as genetics, developmental biology, and neuroscience.  Model organisms are typically chosen for their easy maintenance and reproduction in a laboratory setting, short generation cycles, or the capacity to generate mutants to study certain traits or diseases.

Model organisms provide valuable insights into biological systems at the cell, tissue, organ, and system level. There are several types of model organisms and they vary in complexity and use. Small, simple organisms, such as yeast, are typically used to study gene mutations in human cancers, whereas the fruit fly (Drosophila melanogaster) and the zebrafish (Danio rerio) are ideal for the study of genetics and development of disease. Mouse models are also extensively used in biomedical research to study the progress of disease and development of new drugs.

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Leica Microsystems: Model Organism Imaging

Go from overview to fine detail to enhance the understanding of your model organisms with flexible imaging systems from Leica Microsystems.

Leica Microsystems provides innovative microscopy solutions to achieve optimal image quality. These solutions are applicable even with large and complex specimens, such as model organisms, and include platforms for screening and manipulation.

Mouse embryo

Mouse embryo with THUNDER Imager Model Organism

Neurofilaments stained in red to assess neuronal outgrowth in E12-14 mouse. The mouse was uncleared. Courtesy of Yves Lutz, Centre d’imagerie, IGBMC, France.

Microscopy for Model Organism Research

Model organisms are in most cases large, complex, and dense, which can be a challenge. Therefore, there is a need for flexibility from microscope systems to enable the study of these samples. Traditionally, several microscopy techniques are necessary for the study of model organisms, from stereomicroscopes that enable macroscopic analysis and manipulation of specimens such as zebrafish, to multiphoton microscopes that allow deep imaging of large live organisms.

For these thicker specimens, confocal microscopy is the tool of choice to see detail at depth and avoid out-focus-signals. However, it usually poses several challenges, such as slow speeds and photobleaching due to high laser power.

Innovative techniques, such as light sheet microscopy, are becoming more prominent when imaging these light-sensitive samples in 3D thanks to its low phototoxicity.

Challenges when imaging Model Organisms

Work involving model organisms is very heterogeneous and, as such, challenges when using microscopy techniques vary depending on whether they are used for dynamic studies or the study of molecular events, but it can also depend on the complexity of the model organism used, going from the few cells of C. elegans to large complex animals such as the mouse.

A common challenge encountered when imaging model organisms is speed of throughput. Due to the size of the sample, imaging can involve lengthy acquisition times and the analysis of many images to get a complete dataset, which overall reduces experimental efficiency. Speed of acquisition is also an issue when imaging live model organisms, as phototoxicity and photodamage can result in disruption of the sample’s physiology or even cell or sample death. Finally, imaging points within the deep layers of the sample can also produce image artifacts and blurring.

Zebrafish posterior lateral line primordium migration. Membranes: cyan GFP: Nuclei: magenta, tdTomato. Imaging performed with resonant scanner, Dynamic Signal Enhancement and LIGHTNING. Sample courtesy: Jonas Hartmann, Gilmour Group, EMBL Heidelberg.

Leica Imaging Solutions

Go from overview to fine detail to enhance the understanding of your model organisms with flexible Leica imaging systems.


The STELLARIS 8 DIVE (Deep In Vivo Explorer) is the first multiphoton microscope with spectrally tunable detection. It provides maximum penetration depth and contrast for deep in vivo imaging. With the STELLARIS 8 DIVE, you can tune for the deepest insight and finest detail, while imaging multiple markers with perfect color separation.

Digital LightSheet

The TCS SP8 DLS (Digital Light Sheet) system from Leica Microsystems is an innovative concept which integrates the Light Sheet Microscopy technology into our confocal platform. The combination of low light illumination and high speed acquisition of DLS allows you to observe fast and repeated or intermittent biological processes in three dimensions over an extended time period. For example, you can follow the development of sensitive organisms, such as a Drosophila embryo, over long time periods to understand how tissue and organs form in real time and in 3D.

THUNDER Imager Model Organism

The THUNDER Imager Model Organism allows fast and easy 3D exploration of whole organisms for developmental or molecular biology research. Thanks to Computational Clearing, your images reveal the finest structural details. No hassle with out-of-focus blur while maintaining the capabilities and ease-of-use typical for Leica stereo microscopes.

A THUNDER Imager Model Organism is the optimal instrument for studying, e.g., Drosophila, C. elegans, zebrafish, plants, and mice. One device for screening, positioning, and imaging your specimen. Simplify your workflow and study model organisms from a large overview to the highest detail.

Products related to Model Organism Research

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STELLARIS - Confocal Microscope Platform


With the STELLARIS confocal platform, we have re-imagined confocal microscopy to get you closer to the truth.

THUNDER Imager Model Organism

The THUNDER Imager Model Organism allows fast and easy 3D exploration of whole organisms for developmental or molecular biology research.


The THUNDER Imager EM Cryo CLEM enables precise identification of cellular structures and smooth, secure transfer of coordinates, images, and samples through your correlative workflow.


Explore label-free chemical imaging with Coherent Raman Scattering Microscopy

Multiphoton Microscope STELLARIS 8 DIVE


DIVE and STELLARIS have merged to provide you with the power of flexible multicolor multiphoton imaging.

Digital Light Sheet Microscoep STELLARIS DLS


Discover new applications by combining confocal and light-sheet microscopy

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