Advanced Microscopy Techniques

New Dimensions in Neuroscience

Investigate the Brain in Unparalleled Resolution

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  • Key Benefit 1
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  • Woman wearing ZEISS ClearView glasses faces mannequin wearing glasses.
  • Enhanced Visualization

    Observe brain structure morphology in unprecedented detail.

  • Real-Time Dynamics

    Quantify neural activity at different time scales, deepening understanding of complex processes.

  • Comprehensive Neural Mapping

    Execute comprehensive histological studies, mapping the brain to understand the anatomy of function and disorder.

Are you leveraging the latest innovations?

Discover the techniques that are advancing neuroscience

Studying Synaptic Function

Overcome the diffraction limit by combining super-resolution imaging and advanced processing techniques to visualize synaptic components at the nanoscale.

Cellular Dynamics of Neurodegenerative Disease

Visualize in real-time cellular processes underlying disease progression and identify the critical changes in behavior and morphology to gain a deeper understanding of neurodegeneration.

Studying the Role of Glial Cells

Enhanced optical sectioning capabilities can minimize our-of-focus light, allowing for clearer visualization of glial cell processes and their interactions with neurons and vasculature.

Understanding Neural Circuitry

Light sheet imaging captures data from multiple angles, allowing for thee-dimensional imaging of large samples and whole rodent brains so that researchers can map entire neural circuits and brain vasculature.

Visualize Deep Brain Activity

Image deep in the living brain, obtaining high-resolution images at speed allowing researchers to observe complex dynamics in real-time, mapping circuits to external stimuli.

Revolutionize Brain Studies Integrating advanced microscopy in neuroscience research equips scientists with the tools necessary to investigate the intricate workings of the brain, driving forward our understanding of neurological functions and advancing the quest for effective therapies for neuro-diseases and disorders

Are you leveraging the latest innovations?

Discover the techniques that are advancing neuroscience

Visualize Deep Brain Activity

Image deep in the living brain, obtaining high-resolution images at speed allowing researchers to observe complex dynamics in real-time, mapping circuits to external stimuli.

Studying Synaptic Function

Overcome the diffraction limit by combining super-resolution imaging and advanced processing techniques to visualize synaptic components at the nanoscale.

Understanding Neural Circuitry

Light sheet imaging captures data from multiple angles, allowing for thee-dimensional imaging of large samples and whole rodent brains so that researchers can map entire neural circuits.

Cellular Dynamics of Neurodegenerative Disease

Visualize in real-time cellular processes underlying disease progression and identify the critical changes in behavior and morphology to gain a deeper understanding of neurodegeneration.

Studying the Role of Glial Cells

Enhanced optical sectioning capabilities can minimize our-of-focus light, allowing for clearer visualization of glial cell processes and their interactions with neurons and vasculature.

Are you leveraging the latest innovations?

Discover the techniques that are advancing neuroscience

Studying Synaptic Function

Overcome the diffraction limit by combining super-resolution imaging and advanced processing techniques to visualize synaptic components at the nanoscale.

Cellular Dynamics of Neurodegenerative Disease

Visualize in real-time cellular processes underlying disease progression and identify the critical changes in behavior and morphology to gain a deeper understanding of neurodegeneration.

Studying the Role of Glial Cells

Enhanced optical sectioning capabilities can minimize our-of-focus light, allowing for clearer visualization of glial cell processes and their interactions with neurons and vasculature.

Understanding Neural Circuitry

Light sheet imaging captures data from multiple angles, allowing for thee-dimensional imaging of large samples and whole rodent brains so that researchers can map entire neural circuits and brain vasculature.

Visualize Deep Brain Activity

Image deep in the living brain, obtaining high-resolution images at speed allowing researchers to observe complex dynamics in real-time, mapping circuits to external stimuli.

Why You Do What You Do

  • 1 in 5

    Adults in the United States experiencing mental illness annually

  • 50M

    Number of people worldwide are currently living with dementia, with Alzheimer's disease being the most common form.

  • 1 in 44

    The prevalence of Autism Spectrum Disorder affecting children in the United States.

Complete your lab

with our new solution bundles

You can enhance your Neuroscience Research with the following solutions

Slide Scanning Solutions for Your Field of Application

ZEISS Axioscan 7 configurations are designed to meet your unique requirements.
Paraffin-embedded mouse kidney. Sample courtesy: Florian Gembardt,  University Clinic Carl­Gustav Carus Dresden, Germany
Paraffin-embedded mouse kidney. Sample courtesy: Florian Gembardt,  University Clinic Carl­Gustav Carus Dresden, Germany

Axioscan 7

Scanning performance combined with application freedom
  • Benefit from application flexibility in a multi-user environment.
  • Switch rapidly between fluorescence, brightfield and polarization.
  • Get research-grade data quality for demanding fluorescence applications.
  • Use powerful ZEN software to access many more processing and analysis functions.

Axioscan 7 spatial biology

Scalable multipex imaging for routine applications
  • Speed up multiplex imaging of up to eight fluorescence stained biomarkers.
  • Benefit from solutions for robust, automated tissue detection and hyperplex cyclic imaging assays.
  • Get an optimized configuration for superior inter-day and inter-device reproducibility.
  • Choose from complementary software offerings for lab-automation, LIMS integration and AI-based image analysis.
Multichannel acquisition and machine learning segmentation of Berea Sandstone.
Multichannel acquisition and machine learning segmentation of Berea Sandstone.

Axioscan 7 geology

Thin section slide scanning for digitization of petrography data
  • Digitize geologic collections quickly.
  • Generate complete petrographic data.
  • Collaborate remotely across borders. 
  • Scanning Performance Combined with Application Freedom

    Axioscan 7 combines qualities that you would never expect to find in a slide scanner—things like high-speed digitization and outstanding image quality, plus an unrivaled variety of imaging modes—all wrapped up in a fully automated and easy to operate system. Even the most challenging research tasks are supported by powerful hardware and perfectly featured software. Give your imaging facility users the ability to capture virtual slides quickly and with consistently high quality, whether their applications call for brightfield, fluorescence or polarization imaging.

    A Variety of Super-fast Brightfield Imaging Modes

    A newly designed condenser with its motorized modulator disk lets you switch automatically between different brightfield imaging modes to adapt to the different requirements of your applications. This opens up a whole new range of experiments and modality combinations, with:

    • dramatically improved scan speeds in all brightfield imaging modes
    • better sample detection and focusing
    • new phase and relief contrast options
    • circular and linear polarization now fully supported.
    Mouse kidney wound healing assay, stained with sirius red, brightfield. Sample courtesy: Alexander Lomow, Evotec
    Mouse kidney wound healing assay, stained with sirius red, cross linear polarization. Sample courtesy: Alexander Lomow, Evotec

    Reproducible Image Quality

    ZEISS Axioscan 7 offers reliably reproducible image quality, no matter whether you repeat your imaging task after a day, a week, a month or even on a different machine.

    Paraffin-embedded mouse kidneys from healthy wildtype animals (12 weeks). Nephrin stained with Cy3. PCNA APC (FarRed) and DAPI as counterstaining. Imaged with 20× NA 0.8 objective.

    Paraffin-embedded mouse kidneys from healthy wildtype animals (12 weeks). Nephrin stained with Cy3. PCNA APC (FarRed) and DAPI as counterstaining. Imaged with 20× NA 0.8 objective.

    TIE Contrast

    Improved Detection. Better Focusing. More Context.

    Introducing Transfer of Intensity Equation (TIE), the new contrast method for contrast generation in transparent samples. Now you can record the interaction of a narrow cone of light with your sample’s structures in three images: one in focus and two out of focus above and below the focal plane. From these three images, the phase information for the central plane is automatically extracted. Continuous acquisition in the z dimension, combined with flash illumination and GPU-based fast image processing, enables very fast delivery of the final contrast images. Present this as either phase contrast or DIC-like relief contrast: it’s your choice.

    TIE contrast is an excellent tool that supports your experiments when working with sensitive fluorescent dyes:

    • Detect transparent tissues with little to no contrast in regular brightfield mode.
    • Speed up the subsequent fluorescence imaging process with very fast flash-based focusing.
    • Protect your sensitive dyes from bleaching during focusing by using the lowest light doses.
    • Bring your fluorescent labels into context easily by applying additional contrast information.
    Solanum tuberosum – potatoe starch, 20x Plan-Apochromat 0.8; A) TIE phase contrast, B) TIE relief contrast, C) Brightfield
    Solanum tuberosum – potatoe starch, 20x Plan-Apochromat 0.8; A) TIE phase contrast, B) TIE relief contrast, C) Brightfield

    Solanum tuberosum – potatoe starch, 20x Plan-Apochromat 0.8; A) TIE phase contrast, B) TIE relief contrast, C) Brightfield

    Solanum tuberosum – potatoe starch, 20x Plan-Apochromat 0.8; A) TIE phase contrast, B) TIE relief contrast, C) Brightfield

  • Workflow Automation for Multiplexed Spatial Profiling at Scale

    By leveraging multiplex immunofluorescence (mIF) staining with multiple biomarkers, spatial biology allows simultaneous visualization and quantification of numerous proteins within a single tissue section. This enables detailed analysis of cell presence, abundance, spatial distribution and cell-to-cell interactions.

    Load ZEISS Axioscan 7 spatial biology with 100 samples and scan them all in less than a day with unprecedented speed, fully automated and supported by AI-enabled tissue detection and high dynamic range imaging. Analyze up to eight biomarkers at the same time and generate highly reproducible data that you can rely on. We offer complimentary service solutions to integrate streamlined workflow solutions into pre-existing LIMS and IMS systems.

    Non-small Cell Lung Cancer (NSCLC) Tissue

    The UltiMapper I/O PD-L1 kit from Ultivue looks at whether a tumor is ‘hot‘ or ’cold’. It also addresses whether the tumor will respond to immune checkpoint inhibition because of a high immune filtrate (hot in contrast to tumors with low immune infiltrates ( ‘cold tumors’ or non-T-cell-inflamed cancers). It does this by exploring multiple cell phenotypes such as cytotoxic immune cells (CD8), immunosuppressive macrophages (Markers CD68, PD-L1) or immune evading tumor cells (Markers CK, PD-L1).

    Please note. The following images 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 the Axioscan 7 spatial biology slide scanner.

    NSCLC tissue stained with UltiMapper I/O PD-L1 kit.
    NSCLC tissue stained with UltiMapper I/O PD-L1 kit.

    NSCLC tissue stained with UltiMapper I/O PD-L1 kit.

    NSCLC tissue stained with UltiMapper I/O PD-L1 kit. Picture detail.
    NSCLC tissue stained with UltiMapper I/O PD-L1 kit. Picture detail.

    NSCLC tissue stained with UltiMapper I/O PD-L1 kit. Picture detail.

    Mouse spleen fresh frozen sections, 8-plex staining of CD11c, CD4, F4/80, CD8, CD11b, B220, CD169, DAPI using Kromnigon StreptaClick® technology. DAPI is not shown on this image.
    Mouse spleen fresh frozen sections, 8-plex staining of CD11c, CD4, F4/80, CD8, CD11b, B220, CD169, DAPI using Kromnigon StreptaClick® technology. DAPI is not shown on this image.

    Mouse spleen fresh frozen sections, 8-plex staining of CD11c, CD4, F4/80, CD8, CD11b, B220, CD169, DAPI using Kromnigon StreptaClick® technology. DAPI is not shown on this image.

    Mouse spleen fresh frozen sections. Picture detail.
    Mouse spleen fresh frozen sections. Picture detail.

    Mouse spleen fresh frozen sections. Picture detail.

    Human tonsil FFPE tissue section stained with Ki67, GranzymeB, CD3, CK/SOX10, DAPI.
    Human tonsil FFPE tissue section stained with Ki67, GranzymeB, CD3, CK/SOX10, DAPI.

    Human tonsil FFPE tissue section stained with Ki67, GranzymeB, CD3, CK/SOX10, DAPI.

    A composite image of Non-Small Cell Lung Cancer tissue, stained with Ki67, GranzymeB, CD3, CK/SOX10, DAPI.
    A composite image of Non-Small Cell Lung Cancer tissue, stained with Ki67, GranzymeB, CD3, CK/SOX10, DAPI.

    A composite image of Non-Small Cell Lung Cancer tissue, stained with Ki67, GranzymeB, CD3, CK/SOX10, DAPI.

    Sample is courtesy of Concept Life Sciences, CRO in UK.

    A mouse liver FFPE tissue section stained with 6 biomarker targets and DAPI.
    A mouse liver FFPE tissue section stained with 6 biomarker targets and DAPI.

    A mouse liver FFPE tissue section stained with 6 biomarker targets and DAPI.

    A mouse liver FFPE tissue section. Picture detail.
    A mouse liver FFPE tissue section. Picture detail.

    A mouse liver FFPE tissue section. Picture detail.

    Colon cancer spheroid co-cultured with fibroblasts. FFPE sections stained for Filaggrin, Ki67, Collagen-1, E-cadherin, DAPI. The spheroids were grown, fixed, paraffin embedded, cut and stained at Bioneer A/S (Hørsholm, Denmark)
    Colon cancer spheroid co-cultured with fibroblasts. FFPE sections stained for Filaggrin, Ki67, Collagen-1, E-cadherin, DAPI. The spheroids were grown, fixed, paraffin embedded, cut and stained at Bioneer A/S (Hørsholm, Denmark)

    Colon cancer spheroid co-cultured with fibroblasts. FFPE sections stained for Filaggrin, Ki67, Collagen-1, E-cadherin, DAPI. The spheroids were grown, fixed, paraffin embedded, cut and stained at Bioneer A/S (Hørsholm, Denmark)

    The cancer spheroid shown here contains HT29 colon cancer cells, fibroblasts and bead-activated T cells, and shows a partly disintegrated spheroid structure, where the damage is caused by cytotoxic T-cells (CD8 positive, yellow).
    The cancer spheroid shown here contains HT29 colon cancer cells, fibroblasts and bead-activated T cells, and shows a partly disintegrated spheroid structure, where the damage is caused by cytotoxic T-cells (CD8 positive, yellow).

    The cancer spheroid shown here contains HT29 colon cancer cells, fibroblasts and bead-activated T cells, and shows a partly disintegrated spheroid structure, where the damage is caused by cytotoxic T-cells (CD8 positive, yellow). HT29 cells are stained with the panCK antibody (red). A subset of T cells is PD-1 positive (purple). The fibroblasts remain unstained (dense DAPI-positive structure) except for some Ki67 staining. A subset of CD8⁺ cells is co-expressing Ki67. The spheroids were grown, fixed, paraffin embedded and cut at Bioneer A/S (Hørsholm, Denmark).

    Esophagus FFPE tissue sections stained with different chromogenic pathology staining

    Esophagus FFPE tissue section stained with Movat staining
    Esophagus FFPE tissue section stained with Movat staining

    Movat staining

    Esophagus FFPE tissue section stained with AZAN staining
    Esophagus FFPE tissue section stained with AZAN staining

    AZAN staining

    Esophagus FFPE tissue section stained with Goldner staining
    Esophagus FFPE tissue section stained with Goldner staining

    Goldner staining

    Esophagus FFPE tissue section stained with Weigert-Van Gieson (WvG) staining
    Esophagus FFPE tissue section stained with Weigert-Van Gieson (WvG) staining

    Weigert-Van Gieson (WvG) staining

    Bone Marrow FFPE tissue sections stained with different chromogenic pathology staining (first two of the images showing the normal bone marrow, last two Plasmacytoma infiltrated Bone morrow)

    Bone Marrow FFPE tissue section stained with movat staining
    Bone Marrow FFPE tissue section stained with movat staining

    Movat staining

    Bone Marrow FFPE tissue section stained with Weigert-Van Gieson (WvG) staining.
    Bone Marrow FFPE tissue section stained with Weigert-Van Gieson (WvG) staining.

    Weigert-Van Gieson (WvG) staining

    Bone Marrow FFPE tissue section stained with Goldner staining.
    Bone Marrow FFPE tissue section stained with Goldner staining.

    Goldner staining

    Bone Marrow FFPE tissue section stained with Hematoxylin and Eosin (H&E) staining
    Bone Marrow FFPE tissue section stained with Hematoxylin and Eosin (H&E) staining

    Hematoxylin and Eosin (H&E) staining

  • Thin Section Slide Scanning for Digitization of Petrography Data

    Embrace digitalization with Axioscan 7 and you will not only create high-quality digitized petrography data efficiently. You’ll also gain the advantage of easy data sharing and seamless integration into your geological workflows. With AI-integrated analysis and remote collaboration capabilities, Axioscan 7 empowers geologists and researchers to work together seamlessly from anywhere in the world. Maximize the benefits of modern technology in quantitative petrography and automated analytics.

    Multi-channel Acquisition

    Use different forms of polarization illumination to highlight different features. Plane polarized light (PPL) shows the overall crystal color, habit and pleochroism. Crossed polarized light (XPL) at multiple orientations lets you assess the extinction angle and birefringence. Circular polarization allows maximum birefringence to be observed regardless of grain orientation. All channels are aligned using powerful computational algorithms during acquisition, making the resulting data perfect for subsequent segmentation and analysis.

    Circular Polarization
    Circular Polarization

    Circular Polarization

    Cross Polarized Light (XPL)
    Cross Polarized Light (XPL)

    Cross Polarized Light (XPL)

    Plane Polarized Light (PPL)
    Plane Polarized Light (PPL)

    Plane Polarized Light (PPL)

    The combination of ZEISS Axioscan 7 and ZEISS AI-based segmentation creates the Petrography Analysis Toolbox, or PetPAT
    The combination of ZEISS Axioscan 7 and ZEISS AI-based segmentation creates the Petrography Analysis Toolbox, or PetPAT

    Mineral Phase Analysis

    Combine ZEISS Axioscan 7 with ZEISS AI-based segmentation to enable automated analysis across large numbers of samples. Easy machine learning segmentation lets you label each mineral phase of interest, using an intuitive painting interface while the software builds a model of the mineralogy across your entire sample.

    Automated machine-learning based mineral classification using a single ZEN Intellesis model, applied on two sandstone samples
    Automated machine-learning based mineral classification using a single ZEN Intellesis model, applied on two sandstone samples

    AI-Based Mineral Classification

    Automated machine learning-based mineral classification uses a single ZEN Intellesis model, applied here on two sandstone samples.

    Both modal mineralogy and pore / grain sizes can be measured and automatically reported.

    Full thin-section polarization images. This kyanite-bearing schist has been imaged as part of a digital thin section collection.
    Full thin-section polarization images. This kyanite-bearing schist has been imaged as part of a digital thin section collection.

    PPL-to-XPL

    Full thin-section polarization images. This kyanite-bearing schist has been imaged as part of a digital thin section collection. The upper image shows a single PPL orientation while the lower view shows the capture of the thin section in multiple XPL orientations. This lets a simulated stage rotation observe and analyze extinction angles with the full XPL variation over 90°.

    Close up of a single biotite grain within a granite sample. Sample has been imaged in multiple PPL orientations in order to observe the full range of pleochrosim as the sample is rotated through 180° relative to the polarizer.
    Close up of a single biotite grain within a granite sample. Sample has been imaged in multiple PPL orientations in order to observe the full range of pleochrosim as the sample is rotated through 180° relative to the polarizer.

    PPL-to-Pleochroism

    Close up of a single biotite grain within a granite sample. Sample has been imaged in multiple PPL orientations in order to observe the full range of pleochroism as the sample is rotated through 180° relative to the polarizer.

    Use ZEN Connect to intuitively build correlative projects that start with the data-rich, light microscopy environment from ZEISS Axioscan 7 Geo
    Use ZEN Connect to intuitively build correlative projects that start with the data-rich, light microscopy environment from ZEISS Axioscan 7 Geo

    Correlative Microscopy

    Use ZEN Connect to build intuitive correlative projects that start with the data-rich light microscopy environment from ZEISS Axioscan 7 geology. Here additional phase and geochemical information from ZEISS Mineralogic becomes the next step in a petrological investigation. The sample shown here is a granulite facies metagabbro from near Scourie more, Northwest Scotland.

    The powerful PetPAT orientation analysis package turns entire thin sections into mineral orientation maps
    The powerful PetPAT orientation analysis package turns entire thin sections into mineral orientation maps

    Mineral Orientation Analysis

    The optional PetPAT orientation analysis package turns entire thin sections into powerful mineral orientation maps. Use these datasets in conjunction with mineral segmentation for detailed studies and also to generate grain size distribution data.

    • Use XPL image stacks to calculate the angle at which any given pixel is at maximum or minimum luminance.
    • Then use these data to allow the entire thin section to be mapped for orientation of mineral grains in transmitted light.

Configure your Axioscan 7 for Spatial Biology

Workflow automation for spatial biology at scale

The new Axioscan 7 Spatial Biology Configuration is designed to maximize efficiency, accuracy, and reproducibility for multiplex immunofluorescence (mIF) and high-throughput spatial biology workflows.

FAQs for ZEISS in Neuroscience

  • Yes, ZEISS provides various case studies and application notes that showcase the use of their microscopy systems in neuroscience. Examples include:

    • Imaging Synaptic Structures: Using confocal microscopy to study synaptic connections and plasticity.
    • Neurodegenerative Disease Research: Employing two-photon microscopy to observe changes in neuronal behavior in live animal models.
    • Brain Mapping: Utilizing advanced imaging techniques to visualize brain connectivity and function.
  • ZEISS microscopy solutions enhance neuroscience research by providing:

    • High Resolution: Advanced optics and imaging technologies allow for detailed visualization of neuronal structures and processes.
    • Live Imaging: Many systems are designed for live-cell imaging, enabling the observation of dynamic processes in real-time.
    • Multimodal Imaging: The ability to combine different imaging modalities (e.g., fluorescence and electron microscopy) allows for comprehensive analysis of samples.

    These features facilitate a deeper understanding of neural mechanisms and contribute to advancements in neuroscience.

  • ZEISS offers a variety of microscopy techniques tailored for neuroscience research, including:

    • Confocal Microscopy: Ideal for imaging thick samples and obtaining high-resolution images of cellular structures.
    • Two-Photon Microscopy: Particularly useful for imaging living tissues at greater depths, minimizing photodamage.
    • Electron Microscopy: Provides ultra-high resolution for detailed visualization of neuronal structures.

    These techniques enable researchers to explore complex neural networks and cellular interactions in detail.