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.
  • icon graphic of a microscope
    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.

  • icon graphic of a school of fish
    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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Drosophila Research FAQs

  • Long-term imaging of Drosophila embryos and pupae can be limited by light exposure. ZEISS Lightfield 4D enables instantaneous volumetric imaging using multiple sensors, capturing entire 3D datasets without mechanical z-scanning. This high-speed approach reduces the total light dose, helping to preserve viability while capturing dynamic events like morphogenesis, cell migration, or signal transduction in real time. For slower or gentler acquisitions, Lattice Lightsheet 7 provides complementary low-phototoxicity imaging with selective plane illumination.

  • For screening experiments involving large numbers of embryos, imaginal discs, or tissue samples, ZEISS Celldiscoverer 7 and Axioscan 7 offer automated, high-throughput imaging with consistent quality and reproducibility. These systems are ideal for CRISPR or RNAi phenotype screens, biosensor reporters, or drug-response assays. When paired with arivis Pro, you can streamline analysis with batch quantification, classification, and visualization tools built for scale.

  • Mapping fly brain circuits requires balancing coverage with resolution. ZEISS Lightsheet 7 enables full-volume imaging of the intact adult brain and connected sensory structures. For higher-resolution neuroanatomy or cellular localization, LSM 980 with Airyscan 2 provides exceptional sensitivity and spatial detail. Tools like arivis Pro allow for 3D reconstruction, region annotation, and integration with anatomical reference atlases.

  • ZEISS arivis Pro provides powerful tools for cell tracking, lineage reconstruction, and 3D quantification. Whether you're imaging progenitor migration, tissue morphogenesis, or structural changes across development or disease models, arivis Pro scales seamlessly with lightsheet, confocal, and high-content screening data. Built-in machine learning and AI models help extract meaningful features from complex datasets.

  • Yes. ZEISS offers a full correlative imaging workflows to support connectomics and structural neuroscience. Start by identifying neurons or regions of interest non-destructively using X-ray imaging with ZEISS Xradia Versa or fluorescence microscopy with systems like LSM 980 or Lightsheet 7. These datasets guide targeted volume imaging with ZEISS Crossbeam FIB-SEM, enabling nanometer-scale 3D reconstruction of neuronal architecture and synapses. This multiscale approach allows researchers to link light-based molecular signals with detailed ultrastructure in the same specimen.

  • Biosensors like GCaMP, cAMP, or ROS indicators require sensitive, fast imaging. ZEISS Lightfield 4D allows for high-speed volumetric capture of dynamic signals across tissues without z-scanning delays. For biosensors expressed in localized brain regions or imaginal discs, LSM 980 with Airyscan Fast Mode offers rapid frame rates with excellent resolution and sensitivity, enabling detailed analysis of pathway dynamics or neural activity.

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