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3D imaging and analysis solutions for organoid screening

ZEISS arivis Pro Software Analysis tools tailored for organoid research, including accurate 3D segmentation, quantification, and tracking of cellular dynamics
ZEISS Celldiscoverer 7 High-resolution imaging and advanced analysis capabilities that enable detailed exploration of organoid development, cellular interactions, and functional studies in real-time
ZEISS LSM Lightfield 4D Accelerate 3D Imaging and Screening of Colorectal Cancer Models for Enhanced Drug Response Analysis and Cellular Interactions
ZEISS Lightsheet 7 Explore the complexities of neuronal morphology in 3D
ZEISS LSM 990 Acquire multiple images simultaneously, reducing acquisition time and preserving sample integrity
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5 μm frozen section of mouse spleen simultaneously stained with 7 markers plus DAPI. Imaged on Axioscan 7 spatial biology for spatial transcriptomics analysis.
Inflammation and autoimmunity
ZEISS spatial biology enables multiplex imaging to study tissue inflammation and autoimmune disease mechanisms with high precision and throughput.

Uncovering pathways and cell-types in inflammatory processes

Immuno-Oncology
ZEISS spatial biology solutions enable high-throughput, multiplex imaging to advance biomarker discovery in immuno-oncology research.

Evaluating immunotherapy effectiveness and tumor immune interactions
Infectious Disease and vaccines
ZEISS spatial biology solutions empower immunology research with high-resolution, multiplex imaging for deep immune profiling and tissue analysis.

Mapping immune responses to pathogens and vaccine efficacy
Other applications
ZEISS spatial biology supports multiplex imaging to advance tissue regeneration research with detailed cellular and molecular insights.

● Cardiovascular diseases
● Transplant, GVHD
● Regenerative medicine
● Gastrointestinal Diseases
Metabolic diseases
ZEISS spatial biology tools support multiplex imaging and analysis to uncover tissue-level insights in metabolic disease research.

Investigating tissue-specific metabolic pathways and immune cell infiltration in conditions like diabetes and obesity
Neurology
ZEISS spatial biology solutions enable detailed multiplex imaging to explore neural tissue architecture and biomarkers in neurology research.

Exploring immune-neural interactions and their role in neurological disorders

Drug Development

  • Icon describing target validation

    Target Validation

    Confirms expression & spatial relevance of the target

  • Icon describing mechanism of action studies

    Mechanism of Action Studies

    Confirms how drugs work & their impact on tissue microenvironments

  • Icon describing drug efficacy & pharmacodynamics (PD) studies

    Drug Efficacy & Pharmacodynamics (PD) Studies

    Evaluates treatment effects at the tissue level

  • Icon describing toxicology & safety studies

    Toxicology & Safety Studies

    Detects off-target effects and potential toxicity risks

  • Icon describing predictive biomarkers for patient stratification

    Predictive Biomarkers for Patient Stratification

    Enables personalized medicine & companion diagnostics

  • Icon describing clinical trial monitoring & response assessment

    Clinical Trial Monitoring & Response Assessment

    Tracks drug efficacy & resistance mechanisms over time

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What You Can Do

  • 20 fps

    Recommended imaging speed for GCaMP dynamics

    with ZEISS Airyscan multiplex

  • 40nm

    The approximate size of a synaptic vesicle

    capable on ZEISS Volutome.

  • 5µm

    The average length of a mitochondria

    live imaging using the Lattice SIM family

Product comparison

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See Sierra Oakley’s Scientific Ally

Seek Clarity In Your Subjects

Unlocking new levels of understanding and success in your own education.

Let's get started

Complete your lab

with our new solution bundles

You can enhance your Neuroscience Research with the following solutions

Configure your Stemi 305
Select a category Oncology
Oncology
Immunology
Metabolic Diseases
Neuroscience

Cancer Research

Vesicle Trafficking

In this series "From Image to Results", explore various case studies explaining how to reach results from your demanding samples and acquired images in an efficient way. For each case study, we highlight different samples, imaging system.
Learn More

Looking for One in Many Millions with Automated Imaging

Biopharma researchers develop an automated imaging platform to screen for rare cancer cells in liquid biopsies.
Learn More

Workflow demos for biotech & pharma

Select the demo that suits your needs
  • Virtual demo: Personalized insights into ZEISS technology
  • Demo at ZMCC: Visit ZEISS Microscopy Customer Center (ZMCC)
  • Select your experience: Choose the demo that fits your schedule
Request a Demo

Workflow demos for biotech & pharma

Select the demo that suits your needs
  • Virtual demo: Personalized insights into ZEISS technology
  • Demo at ZMCC: Visit ZEISS Microscopy Customer Center (ZMCC)
  • Select your experience: Choose the demo that fits your schedule
Request a Demo

Microscopy demos for biotech & pharma

Select the demo that suits your needs
  • Virtual Demo: Personalized insights into ZEISS technology
  •  Demo at ZMCC: Visit ZEISS Microscopy Customer Center (ZMCC)
  • Select your experience: Choose the demo that fits your schedule
Request a Demo

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Enabling Efficient, Reproducible Multiplex Spatial Profiling at Scale

Are you a translational, immuno-oncology researcher or service laboratory looking for a comprehensive solution that enables you to work at high throughput while ensuring accurate and reproducible data? The ZEISS tissue multiplexing workflow for biopharma, Academic Medical Centers and CROs enables routine histopathology laboratories with no prior experience of spatial biology methods to deliver rich biomarker data with high consistency across large cohorts.

Benefit from the efficiency of this tissue multiplexing workflow in your large cohorts, even under tight deadlines. Standardized methods allow you to conduct multi-site clinical trials with consistency over time, ensuring reproducible and consistent results. In addition, our solution streamlines data analysis and reporting, making it easier to evaluate multiple parameters and gain actionable insights.

Heartbeat of zebrafish, nuclei tracked
Courtesy of Stone Elworthy and Emily Noël, data acquired at Wolfson Light Microscopy Facility, School of Biosciences at the University of Sheffield, UK.

Cell Biology: Quantify with Precision​

From single cells to comprehensive populations, extract meaningful data automatically​

Transform your cell biology research with ZEISS arivis's powerful quantification capabilities for complex cellular phenotypes. Easily segment, track, and analyze heterogeneous cell populations in complex microenvironments that better mimic in vivo conditions. Obtain reproducible measurements that capture subtle phenotypic changes without manual intervention. ​

  • Easily automated cell and nuclei counting with AI-based segmentation​
  • Cell or nuclei tracking across time series to analyze division and migration​
  • Confluency measurement for growth monitoring​
  • Phenotypic classification based on multiple parameters​ using AI or custom feature patterns​
  • Quantification of cell-cell relationships, such as distance measuerments and colocalization​
  • Batch processing for batch and high-content experiments

Related Applications

Configure your arivis Pro Software

Advanced Image Analysis Made Easy with ZEISS

Explore our software solutions bundles available for trial and purchase online.

Configure your arivis Pro

ZEISS Spatial Biology Solutions

Automated whole slide imaging for consistent results

Turn complexity into clarity and enhance your research capabilities. ZEISS solutions for spatial biology facilitate the seamless integration of spatial profiling into your workflows, ensuring efficient and consistent multiplexed spatial profiling at scale. We accelerate research to better insights and transform the understanding of cellular systems to revolutionize pathology.

Learn more

From complexity to clarity

Workflow automation for spatial biology at scale

ZEISS solutions for spatial biology facilitate the seamless integration of spatial profiling into your workflows, ensuring efficient and consistent multiplexed spatial profiling at scale.

 

ZEISS spatial biology solutions

Complete your lab

with our new solution bundles

Enhance your cancer research with ZEISS solutions

Configure your Axiovert 5

From complexity to clarity

Workflow automation for spatial biology at scale

ZEISS solutions for spatial biology facilitate the seamless integration of spatial profiling into your workflows, ensuring efficient and consistent multiplexed spatial profiling at scale.

 

ZEISS spatial biology solutions

Flexible leasing for microscopes

Invest in cutting-edge technology

ZEISS offers flexible leasing and financing solutions, which enables biotech, pharmaceutical, and research institutions to access world-class imaging systems without the financial strain of high upfront costs.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.

Request a lease now

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.

Configure your Axioscan 7 for Spatial Biology

Schedule Your Demo

See ZEISS Technology in Action

request a demo tailored to your needs—whether virtual or in-person at the ZEISS Microscopy Customer Center (ZMCC). Choose the experience that works best for you!

Schedule a Demo

Workflow demos for biotech & pharma

Select the demo that suits your needs
  • Virtual demo: Personalized insights into ZEISS technology
  • Demo at ZMCC: Visit ZEISS Microscopy Customer Center (ZMCC)
  • Select your experience: Choose the demo that fits your schedule
Request a Demo
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Diagram explaining the end-to-end spatial biology workflow starter bundle ​
Staining Ultivue 4-Plex T-Act Kit​
Image of Ultivue 4-Plex T-Act Kit​

Pre-optimized panel with verified reagent performance and superior staining protocol for best speed and ease-of-use​.
Imaging Axioscan 7 spatial biology

Optimized configuration with best performance for routine spatial biology proteomics workflows​
Configure your Axioscan 7
Imaging SlideStream annual license​
Screenshot of SlideStream, intuitive workflow manager software for scan and analysis automation

Streamlined, fully automated image acquisition experience, with seamless integration for Ultivue scan protocols and automated image transfer to mindpeak platform.​
Analysis Mindpeak starter license​

- Includes access and Spatial Biology research platform, Image Viewer, Image Storage and Data Analysis Platform​

- AI-Powered Image Analysis Algorithms​

- 6 months , 0.5Tb , 25 images can be analyzed​
  • Headshot of Prof. Christoph Kuppe, image copyright Peter Winandy

    The seamless integration of reagents, Axioscan 7, SlideStream, and Mindpeak analytics offers an incredibly user-friendly and fully automated workflow. It has transformed the way we generate spatial phenotypic data; fast, reproducible, and scalable for our clinical research.

    Prof. Christoph Kuppe, MD, PhD University Clinic RWTH Aachen
  • Headshot of Christopher Mills

    A key bottleneck in any spatial biology project is whole-slide tissue scanning, which can lead to unplanned reviews and repeat imaging, making it difficult to predict delivery timelines and associated costs. ZEISS is addressing this challenge with an efficient and reproducible automated workflow that truly benefits CROs offering this service. I’m thrilled to be collaborating with ZEISS in advancing scanning technology and delivering superior outcomes for our clients.

    Christopher Mills Senior Scientist, Concept Life Sciences (CRO in United Kingdom)
  • High Quality Multiplex Data

    See More: Higher Quality Multiplex Data

    Orders of magnitude greater signal amplification; signal-to-noise ratio of up to 30:1.

  • Accelerated, Flexible Data Creation

    See Faster: Accelerated, Flexible Data Creation

    Build, deploy and iterate panels 3x faster, saving months – year(s) of time.

  • More Robust, AI-Driven Insights

    See In Situ: More Robust, AI-Driven Insights

    Deeper insights from state-of-the-art, AI-enabled spatial image analysis.

Focal Adhesion in Vivo

Focal Adhesion In Vivo

with Dr. Minna Roh-Johnson

Understanding how melanoma cells migrate requires in vivo study.

Central to the issue is focal adhesion, or how cancer cells attach to an underlying substrate. Despite years of research, the organization of these structures is still unclear.

Zebrafish earn their stripes

Dr. Roh-Johnson’s lab has developed an innovative system in zebrafish larvae that allows them to observe the formation of focal adhesion structures in highly migratory melanoma cells on the surface of the skin.

Tracking melanoma in zebrafish

They have used this system to dissect the composition and dynamics of focal adhesion structures and have identified unique properties of cancer cells in their native environments. This deeper understanding of focal adhesion formation is a positive step toward therapies to prevent it.

Demos & Leases

Microscopy Demos for Biotech & Pharma

Virtual, Hands-On & Personalized Education & Training

ZEISS provides flexible, tailored demo experiences to showcase its cutting-edge microscopy solutions for biotech and pharmaceutical research. Whether you're remote or onsite, our experts bring the technology—and the insights—directly to you:

  • Virtual Demos offer curated, guided sessions led by ZEISS application specialists. Experience live walkthroughs of systems and software, tailored proof-of-concept experiments using sample data, and application training—all without leaving your lab.
    Zeiss
  • In-Person Demos at the ZEISS Microscopy Customer Center (ZMCC) allow hands-on interaction with the full range of ZEISS imaging platforms. Benefit from personalized consultations, workflow testing with your own or provided samples, and one-on-one support from our specialists.
Revolutionizing IVF Research With state-of-the-art technologies such as super-resolution microscopy, confocal microscopy, and advanced fluorescence imaging, ZEISS microscopes enable researchers to observe cellular and subcellular structures with exceptional clarity and precision. These advancements facilitate a deeper understanding of embryonic development, gamete interaction, and cellular dynamics, ultimately improving the success rates of IVF procedures. By leveraging ZEISS' cutting-edge microscopy techniques, scientists can achieve more accurate diagnoses, optimize treatment protocols, and contribute to the overall progress in reproductive medicine.

Revolutionizing fertility

Breakthroughs in IVF research transforming family dreams

Visualize critical structures like the zona pellucida, polar body, and meiotic spindle with advanced contrast techniques

including circular polarization, PlasDIC and iHMC, while maintaining temperature stability and ergonomic control throughout ICSI, IMSI, and embryo assessment.

Leverage ZEISS developed iHMC for clear visualization of fine cellular details

Especially the nucleus, nucleoli, and nuclear shape within embryos

Ensure precise ICSI timing and optimal oocyte selection

With non-invasive spindle imaging

Streamline semen analysis

With high-resolution imaging, smart documentation, and versatile contrast modes so you can work faster, with greater confidence.

Organoid Research Use Cases

Resources, Articles & More
Select a category High Content Imaging
High Content Imaging
Cancer Research
Drug Discovery & Development

3D preview of analysis results in which individual cells in the outer layer of an organoid are visualized in different colors

‍This solution can be used to segment organoids, their lumen, and nuclei within the organoids using a combination of AI tools and conventional image analysis steps in ZEISS arivis Pro. Using the nuclei masks, the cell bodies of the individual cells within the outer layer of the organoids are segmented.
Learn more

High Content Analysis For Biotech and Pharma

The tools and capabilities you need to drive groundbreaking discoveries, accelerate drug development, and unlock new frontiers in scientific exploration.​
Learn more

High Content Imaging for Genotoxicity

In this series "From Image to Results", explore various case studies explaining how to reach results from your demanding samples and acquired images in an efficient way. For each case study, we highlight different samples, imaging systems, and research questions. In this second episode, we set up an application example to perform DNA-damage analysis by employing ZEISS Axio Observer and the ZEISS arivis Pro image analysis software.
Learn more

ZEISS Axioscan 7

Discover high-performance digital slide scanning tailored to your application needs. Whether your focus is spatial biology at scale, life science research, clinical applications or geology, the Axioscan 7 slide scanning microscope brings you advanced automation capabilities and exceptional image quality.
Learn more

ZEISS Celldiscoverer 7

If your research requires explorative high-content imaging, you are often faced with a trade-off between the desired image quality and the need to capture large amounts of data efficiently. ZEISS Celldiscoverer 7 is your research companion for collecting statistically relevant data, giving you easy access to high-quality imaging, adaptability to demanding experiments, and stable long-term operation.
Learn more

Brain Tumor Microenvironment Spatial Biology with High-Throughput Hyperplexed Imaging

Dr. Spencer S. Watson, a Research Fellow in Professor Joyce’s lab, published an article investigating how the brain tumor microenvironment responds to radiotherapy, not just in terms of changes in different cell populations, but also regarding how the cells spatially organize themselves. In order to do this, the team worked to create a new multiplex workflow, called Hyperplexed Immunofluorescence Imaging (HIFI), to study the spatial biology of tumors before and after treatment.
Learn more

7 Color Multiplex Immunofluorescence Protocol for Spatial Biology with a Digital Slide Scanner

Dr. Caroline Bouzin is the facility manager of the 2IP Imaging Platform at the Institute of Experimental and Clinical Research at the UCLouvain, Brussels, Belgium. She has worked with oncologists and pulmonologists to fine-tune a protocol for customized mIF stainings on formalin-fixed paraffin-embedded (FFPE) tissue samples followed by data collection with the ZEISS Axioscan digital slide scanner. A combination of signal amplification (TSA) with carefully selected filtersets matched to a panel of seven fluorophores results in the fast generation of ready-to-analyze digital images without the need for image post-processing, such as spectral unmixing or tissue alignment. This workflow is equipping researchers in her facility for high-throughput, spatial biology analyses, such as the immune microenvironment of tumors.
Learn more

Spatial Biology Imaging Systems

From Complexity to Clarity: Workflow Automation at Scale
Learn more

From Image to Results | Organoid Analysis

In this new series "From Image to Results", explore various case studies explaining how to reach results from your demanding samples and acquired images in an efficient way. For each case study, we highlight different samples, imaging systems, and research questions.
Learn more

Advanced Microscopy for Biotech & Pharma

From 3D-cellular imaging to tissue analysis for pre-clinical studies, our devices deliver the precision, scalability, and automation needed to drive regulatory-compliant drug discovery workflows.
Focal Adhesion in Vivo

Focal Adhesion In Vivo

with Dr. Minna Roh-Johnson

Understanding how melanoma cells migrate requires in vivo study.

Central to the issue is focal adhesion, or how cancer cells attach to an underlying substrate. Despite years of research, the organization of these structures is still unclear.

Zebrafish earn their stripes

Dr. Roh-Johnson’s lab has developed an innovative system in zebrafish larvae that allows them to observe the formation of focal adhesion structures in highly migratory melanoma cells on the surface of the skin.

Tracking melanoma in zebrafish

They have used this system to dissect the composition and dynamics of focal adhesion structures and have identified unique properties of cancer cells in their native environments. This deeper understanding of focal adhesion formation is a positive step toward therapies to prevent it.

Brightfield Workflow

This content includes an interactive product tour from Tourial that may collect usage data. You can view Tourial's privacy policy for more information.

Fluorescence Workflow

This content includes an interactive product tour from Tourial that may collect usage data. You can view Tourial's privacy policy for more information.

In-Booth Presentations

Attend educational presentations in the ZEISS booth.

  • Super-resolution imaging of the membrane-associated periodic skeleton in neurons uncovers constitutive dynamics

    Presented by Evan Heller, Research Associate in Chemistry and Chemical Biology, Harvard University

    Description....

    Evan Heller, PhD.

    Add bio

  • TITLE

    Presented by Dr, Rose Creed, University of California San Francisco 

    Rose Creed, PhD

    Rose B. Creed is a postdoctoral fellow at the University of California, San Francisco, in the laboratory of Alexandra Nelson, M.D., Ph.D. There, she takes a systems neuroscience approach to examine how impairments in the basal ganglia circuit underlie different types of movement disorders. Rose obtained her Bachelor of Science degree in Biology at Stetson university in 2014 and received her Ph.D. from the University of Alabama at Birmingham (UAB) in summer 2020. While at UAB she worked in the labs of Drs. Matthew Goldberg and Lori McMahon, investigating how loss of function of the mitochondrial targeted kinase PINK1 impacts the striatal circuit and its implication for Parkinson’s disease.

Take the Next Step to Starting Your Own Digital Classroom

Fill out the form below to get started on setting up your own digital classroom. A ZEISS representative will be in contact to answer any questions you have or to help get you started!

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Request a trial

Please fill this form to request a 30-day arivis Pro free trial.

Form is loading...

Please enter a valid email address and avoid typing errors. For trial creation the data entered will be passed on to Carl Zeiss Microscopy GmbH, which is part of the ZEISS Group. 

If you want to have more information on data processing at ZEISS please refer to our data privacy notice.