Apotome optical section and Apotome Plus processed image of transgenic zebrafish larvae at 4 days post fertilization staining for: Glial fibrillary acidic protein, acetylated Tubulin, GFP and DNA. Embedded in 1.2% low melt agarose
H. Reuter, Leibniz-Institute on Aging – Fritz-Lipmann-Institut e.V. (FLI), Germany
Use Case

Zebrafish Research

From development to disease models, explore the full potential of zebrafish using tools for deep, dynamic, and reproducible imaging.

Advanced Microscopy for Zebrafish Development, Disease, and Discovery

ZEISS microscopy systems empower researchers to explore zebrafish biology with exceptional resolution, speed, and flexibility. Whether you're tracking cardiac dynamics, mapping neural activity, analyzing cell migration, or screening drug responses, ZEISS tools support gentle live imaging, deep-tissue visualization, and high-throughput workflows. From whole-organism development to targeted disease models, our systems and software—like Lightfield 4D, Airyscan, Celldiscoverer 7, and arivis Pro—enable reproducible, data-rich imaging at every scale of zebrafish research.

  • Long-Term Developmental Studies Require Gentle, Lasting Imaging

    ZEISS microscopy enables fast, low-stress volumetric imaging—minimizing photodamage to support extended observation of delicate model organisms like zebrafish.

  • Don’t Miss a Beat: Capture Rapid Biological Events in Real Time

    ZEISS imaging solutions combine high speed and resolution to visualize fast, transient processes—like heartbeats or calcium signaling—with clarity and precision in 4D.

  • Make Sense of Big Data from Complex Imaging Experiments

    ZEISS software solutions streamline the management, analysis, and visualization of large datasets—making stitching, tracking, and quantification easier and more efficient.

  • Although zebrafish are optically accessible for in vivo imaging of Shigella infection, they are still whole animals. This makes studies involving high-throughput and high-resolution microscopy challenging and time-consuming. With Celldiscoverer 7 and the arivis AI-enhanced workflow, we can image and analyze a lot more samples at a much faster pace.

    Dr. Serge Mostowy Principal Investigator and Research Team Lead at the Department of Infection Biology, London School of Hygiene & Tropical Medicine, UK
  • We are interested in understanding how innate immune cells known as microglia shape the healthy brain. Our goal is to identify key cellular and molecular processes that regulate postnatal synaptic development in hopes to inform new immune-based therapies for psychiatric and neurodevelopmental illnesses.

    Dr. Anna Molofsky Associate Professor, Weill Institute for Neurosciences at the University of California, San Francisco, USA

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Zebrafish Research FAQs

  • Zebrafish embryos are optically transparent, making them ideal for live imaging—but prolonged exposure to light can still lead to phototoxicity and photobleaching. ZEISS Lightsheet 7 and Lightfield 4D systems use gentle illumination strategies that minimize light exposure while still providing high-speed, volumetric data. These systems are ideal for tracking morphogenesis, organ development, and cell migration across extended time-lapse experiments, even over multiple days.

  • Capturing rapid motion like cardiac contractions or twitching tissues requires both speed and stability. ZEISS Lightfield 4D enables instantaneous 3D volume capture—perfect for recording every beat of the zebrafish heart without motion artifacts. For fluorescent reporters or biosensors in dynamic tissues, Airyscan Fast provides exceptional temporal resolution with enhanced signal-to-noise, making it ideal for imaging fast biological events in developing zebrafish.

  • Yes. Zebrafish are widely used for functional imaging due to their transparency and genetic accessibility. ZEISS Airyscan Fast and Lightfield 4D systems allow researchers to image biosensor activity—such as calcium, cAMP, or voltage indicators—with high sensitivity and speed. These systems support volumetric imaging of the brain or spinal cord in real time, making them powerful tools for studying neural circuits, sensory processing, and pharmacological effects in vivo.

  • Zebrafish studies often generate complex 4D datasets across multiple samples, conditions, or time points. ZEISS arivis Pro is built to handle these challenges, offering robust tools for stitching, segmentation, cell tracking, and batch quantification. Whether you’re analyzing a single embryo over 12 hours or hundreds of wells from a screening run, arivis Pro provides scalable, reproducible workflows that help you extract actionable data from even the largest experiments.

  • For large-scale experiments like toxicity testing, phenotype analysis, or drug discovery, automation and consistency are critical. ZEISS Celldiscoverer 7 and Axioscan 7 provide streamlined, high-content imaging of embryos and larvae in standard multi-well plates or slides. These platforms combine automated acquisition with standardized optics, enabling reproducible results across replicates and conditions. Pairing them with arivis Pro adds automated quantification, making them ideal for both academic and industrial screening pipelines.

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