Mouse brain stained with a lipid dye to mark vasculature membranes, cleared with iDISCO+ and imaged with light sheet microscopy. Sample courtesy of E. Diel, Harvard University, USA
Microscopy Applications for Live Sciences

Chemically Cleared Brain and Thick Tissues

Looking Deep Into Your Samples

With the rise of optical tissue-clearing techniques, voluminous specimens such as entire brains, organs or large model organisms can be imaged with cellular to subcellular resolution without the need for traditional, physical sectioning. This development has been critical for researchers investigating anatomy, vasculature, neural networks or connectomics.

Optical clearing methods, together with computing power, data storage capacity, intelligent rendering and analysis algorithms, and with the right microscopy technology, enable efficient analysis of these large samples.

Mouse kidney cleared with iDISCO protocol and imaged with light sheet microscopy. Sample courtesy of U. Roostalu, Gubra, Denmark.
Mouse kidney cleared with iDISCO protocol and imaged with light sheet microscopy. Sample courtesy of U. Roostalu, Gubra, Denmark.

Mouse kidney cleared with iDISCO protocol and imaged with light sheet microscopy. Sample courtesy of U. Roostalu, Gubra, Denmark.

Mouse kidney cleared with iDISCO protocol and imaged with light sheet microscopy. Sample courtesy of U. Roostalu, Gubra, Denmark.

Balance Large Sample Size, High Resolution Imaging and Fast Acquisition Speed with Light Sheet Microscopy

Light sheet fluorescence microscopy (LSFM) uses a unique illumination method to excite and collect entire planes of data at one time. With cleared samples, this means collecting amazingly high-resolution data throughout a large sample at extremely high speeds. ZEISS Lightsheet 7 equips you for fast imaging of chemically cleared brain, organs or large tissue sections.

  • Human brain organoid with ECi clearing

    to study neuronal morphology

    Imaged with light sheet microscopy. Sample courtesy of D. Reumann and J. Knoblich, Institute of Molecular Biotechnology (IMBA) of the Austrian Academy of Sciences, Austria

  • Mapping interneurons and Purkinje cells

    from an entire mouse brain cleared using the CLARITY protocol.

    Imaged using light sheet microscopy. Sample courtesy of E. Diel and D. Richardson, Harvard University, USA

  • Axolotl forearm

    Cleared in ethyl cinnamate to study vertebrate limb regeneration

    Sample courtesy of W. Masselink, Research Institute of Molecular Pathology, IMP.
    Image courtesy of P. Pasierbek, K. Aumayr, IMP BioOptics, Vienna, Austria

Mouse brain cleared with the CLARITY protocol
Mouse brain cleared with the CLARITY protocol

Mouse brain cleared with the CLARITY protocol and imaged with confocal microscopy. Sample courtesy of T. Ruff, Max Planck Institute of Neurobiology, Germany.

Mouse brain cleared with the CLARITY protocol and imaged with confocal microscopy. Sample courtesy of T. Ruff, Max Planck Institute of Neurobiology, Germany.

Achieve Incredible Resolution and Structural Detail in Cleared Samples with Confocal Microscopy

Confocal microscopy reveals minute, subcellular details and high-resolution structural information from deep within chemically cleared brains, organs or other tissues. The ZEISS LSM 9 confocal family with Airyscan is equipped with super-resolution capabilities and multiplex mode for enhanced acquisition speeds to quickly image the finest structures.

Cleared mouse brain. Upper right: Whole brain overview.
Cleared mouse brain. Upper right: Whole brain overview.

Cleared mouse brain. Upper right: Whole brain overview. Left: Maximum intensity projection (MIP) of a brain region. Lower right: Detail from MIP inset. Acquired with zoom microscopy and structured illumination for optical sectioning. Sample courtesy of Erturk lab, Ludwig Maximilian University of Munich, Germany

Cleared mouse brain. Upper right: Whole brain overview. Left: Maximum intensity projection (MIP) of a brain region. Lower right: Detail from MIP inset. Acquired with zoom microscopy and structured illumination for optical sectioning. Sample courtesy of Erturk lab, Ludwig Maximilian University of Munich, Germany

Large Overview Imaging with Cellular Resolution

Zoom microscopy with chemically cleared brain or large tissue samples enables cellular resolution within very large fields of view. The ZEISS Axio Zoom.V16 zoom microscope can provide you with a large, overview image and then allow you to zoom in and observe single cells within cleared tissues. Equip Axio Zoom.V16 with ZEISS Apotome 3 to add optical sectioning and enhanced structural information.

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    * The images shown on this page represent research content. ZEISS explicitly excludes the possibility of making a diagnosis or recommending treatment for possibly affected patients on the basis of the information generated with an Axioscan 7 slide scanner.