Skip to main content
Research Microscopy Solutions
back
Research Microscopy Solutions
recommended searches
popular searches
Desktop monitor showing a screen of the ZEISS arivis Pro software with analysis results of nuclear pore complexes of FIB-SEM volume electron microscopy data.
Software

ZEISS arivis Pro

Your Solution for Advanced Image Analysis and Visualization

Maximize your image potential with our powerful image analysis and visualization tools. Create seamless analysis pipelines with just a few clicks. Effortlessly process massive datasets on compatible workstations. “Walk into your sample” using our VR toolkit for a new perspective.

  • Click-and-play solution for routine or customized workflow
  • Combine different operators for flexible pipelines
  • Compatible with multiple imaging file formats
  • Supports customized and open source AI models
  • Visualize big data by GPU powered 3D engine
A female scientist who works in a microscopy lab is looking at a desktop monitor showing a screen of the ZEISS arivis Pro software with analysis results of nuclear pore complexes of FIB-SEM volume electron microscopy data. Two other scientists are in the background.

Powerful Interactive Tools to Create Flexible Pipelines

ZEISS arivis Pro enables you to easily create flexible image analysis and visualization pipelines to answer your research questions. Leverage traditional methods or AI models effortlessly to create pipelines for any image size, dimension, or modality without the need to code.

The software supports and handles over 30 commercial file formats. Efficiently process large files with ease. Pre-configured pipelines and standard assays are available for both simple and demanding analysis tasks. Or you can customize pipelines for your specific goals.

It takes just one click to repeat your analysis for consistent, quantitative results. Boost productivity and ensure reproducible results.

Request a Demo
Sub cellular analysis based in AI model of FIB SEM image

Sub cellular analysis based in AI model of FIB SEM image

Sub cellular analysis based in AI model of FIB SEM image
Courtesy of Anna Steyer and Yannick Schwab, EMBL.
Courtesy of Anna Steyer and Yannick Schwab, EMBL.

Advanced 3D Analysis

Boost results quickly with AI for multidimensional image analysis. Annotate slices in your Z-stack to train your model for image segmentation and classification, and then apply it to the whole dataset. Use Machine Learning and Deep Learning operators locally or train models in the cloud and then import them to form the core of your flexible pipeline or assay. Visualize results in 3D and create videos for a polished analysis report with a few clicks.

3D organoid analysis

3D organoid analysis

3D organoid analysis
Sample courtesy of Lutholf lab, imaging by Frank Vogler in the ZEISS customer center

High Content Analysis

Drug discovery demands advanced image analysis methods such as screening against a broader view of cell or tissue phenotype, scalable from 2D to 4D. Train an AI model using ZEISS arivis software on the cloud or locally, and automate image analysis to save time, reduce human bias, and gain consistent results.

Tracking with ZEISS arivis Pro VR

Tracking with ZEISS arivis Pro VR

Tracking with ZEISS arivis Pro VR

Tracking and Lineage

Quantify cell division and migratory phenotypes, and track changes in 2D and 3D image sets of any size. Use ZEISS arivis Pro VR to accurately proofread automatically generated tracks in an immersive VR environment. Easily reapply your pipeline to more datasets.

Automated 3D neuron tracing of neuronal tissue (mouse brain).

Automated 3D neuron tracing of neuronal tissue (mouse brain).

Automated 3D neuron tracing of neuronal tissue (mouse brain). Courtesy of Dr. Steffen Burgold, ZEISS RMS Customer Center Oberkochen, Germany.
Courtesy of Dr. Steffen Burgold, ZEISS RMS Customer Center Oberkochen, Germany.
Courtesy of Dr. Steffen Burgold, ZEISS RMS Customer Center Oberkochen, Germany.

Neurobiology

Deploy cutting-edge neuron tracing algorithms for automatic, repeatable analysis of diverse images with a single click. Quantify neurons, glia/ microglia cells, axons, and more, even with low signal-to-noise ratio (SNR). Edit traces easily, using our semi-automatic interactive and VR tools. Analyze past experiment data, no matter the image format.

30-day old octopus. Sample courtesy of Montserrat Coll Lladó, Jim Swoger/EMBL Barcelona and Roger Villanueva/ICM-CSIC
30-day old octopus. Sample courtesy of Montserrat Coll Lladó, Jim Swoger/EMBL Barcelona and Roger Villanueva/ICM-CSIC
30-day old octopus. Sample courtesy of Montserrat Coll Lladó, Jim Swoger/EMBL Barcelona and Roger Villanueva/ICM-CSIC
30-day old octopus. Sample courtesy of Montserrat Coll Lladó, Jim Swoger/EMBL Barcelona and Roger Villanueva/ICM-CSIC

ZEISS arivis Pro VR Toolkit

Get a new perspective on your sample with an immersive virtual reality experience. Freed from being tethered to your keyboard and mouse, you can directly move, rotate, scale, and shape your digital image data. Experience an in-depth perception equivalent to the real world.

  • Explore your sample in 3D
  • Observe details from diverse angles
  • Collaborate with colleagues for a live review of your sample and results
  • Easy voice and hands-on control
  • Effective, interactive proofreading and editing of automatic analysis results.
Convert Over 30 Image File Formats

Convert Over 30 Image File Formats

No matter what instrument you used to create your image, which format or file size: the ZEISS arivis SIS Converter easily converts your image file to our Scalable Image Storage (SIS) format, for fast and interactive exploration of your images with ZEISS arivis Pro, arivis Pro VR and arivis Hub. Save considerable time, while retaining all the data for advanced analysis.

  • Supports file conversion for over 30 formats
  • Que several import and conversion tasks
  • Unattended batch conversion
  • User-friendly file conversion task management interface
  • Not only microscopy images (e.g., CT, MRI)

Newest arivis Pro Release Highlights

Find out if you can benefit from the latest features available with the most current ZEISS arivis Pro release.

  • Third-party Content Blocked

    The video player is blocked due to your cookie preferences. To change the settings and play the video, please click the button below and consent to use of "Functional" tracking technologies.

    AI-powered Multiwell Analysis Support with ZEISS arivis 4.4
    Released 30 September 2025

    • Multiwell Batch Processing: Optimize analysis pipelines across multiple wells and fields with real-time monitoring, seamless navigation, and direct upload to arivis Hub for scaled parallel processing.
    • AI-assisted Annotations: Accelerate object labeling and deep learning training with AI assistance. Streamline manual 3D segmentation using AI-assisted 2D slice annotation combined with automatic interpolation.
    • Cellpose-SAM Foundation Model: Access expert-level biological segmentation with improved reliability across varying imaging conditions including different channels, cell sizes, noise levels, resolution, and blur.
    • Enhanced 4D Visualization and Faster Movie Export: Intuitive image rotation controls, adjustable clipping plane angles with simple handles for exploring volumes from any perspective, and Quick Movie Mode for up to 15x faster video creation. VR support now includes neuron tracing results and spines.
  • Spines traced and segmented on neuron microscopy image
    Spines traced and segmented on neuron microscopy image

    Image Analysis Made Even Easier with ZEISS arivis Pro 4.3
    Released 11 March 2025

    ZEISS arivis Pro 4.3 brings significant enhancements to image analysis capabilities. Here's a summary of the key new features.

    Core Enhancements:

    • AI-assisted Spine Tracing: Advanced neuronal structure analysis through automated spine detection using pretrained AI models as well as classical approaches
    • Enhanced Cell Measurements for HCA: Expanded measurement capabilities enabling richer feature sets for Cell Painting and other High-Content Analysis (HCA) applications
    • Native CZI Support: Ensures format consistency across ZEISS imaging and analysis platforms while streamlining workflows through direct file processing, with no intermediate conversion steps needed
    Overcoming the ‘Pancake effect’
    Overcoming the ‘Pancake effect’

    Additional Improvements

    • Support New File Formats: Expands arivis Pro's ability to read multiple microscopy file formats, supporting facilities that use different imaging platforms.
    • Performance Optimization: for Deep Learning 
      • Faster deep learning processing for instance segmentation
      • Improved shared memory utilization
      • Extended instance segmentation support for virtual machines and ZEISS arivis Hub
    • Preview for Local Deep Learning Trainer: Enables users to evaluate the segmentation quality of a trained model plane-wise, providing immediate feedback on its performance without requiring the execution of a full 3D analysis pipeline
    • Visualization Improvements: Enhanced surface rendering in 4D Viewer creates more natural-looking 3D visualizations, especially benefiting instance segmentation results by eliminating the "stacked" appearance of segmented objects

  • Third-party Content Blocked

    The video player is blocked due to your cookie preferences. To change the settings and play the video, please click the button below and consent to use of "Functional" tracking technologies.

    Customization at the Forefront of Microscopy Image Analysis
    Released 19 June 2024

    ZEISS arivis Pro 4.2 offers users the freedom to select the most suitable image analysis method for their needs.

    The new release includes enhanced AI-driven tools, 3D analysis capabilities, and large dataset handling. The software allows for unprecedented flexibility to tailor microscopy image analysis workflows to answer research questions.

    Watch this short video to learn more about the newest features.

    drip cellpose

    drip cellpose

    drip cellpose

    What's in it

    New & Noteworthy:

    • Optimized meshing and rendering for unlimited numbers of objects in the 4D Viewer 
    • Instance (object-based) segmentation driven by Deep Learning models trained on ZEISS arivis Cloud
    • Cells and nuclei segmentation in microscopy images using the Cellpose operation 
    • High precision preview in the Analysis Pipeline can work on 3D data to produce a more meaningful preview 
    • Analysis can directly show a preview in the 4D Viewer for object creation operations (e.g. Neuron Tracer) 
    • Machine Learning can auto-optimize the used feature set (to improve performance) 
    • Improved handling for huge amounts of objects in the objects table 
    • Rebranding is completed: The software is now called ZEISS arivis Pro

Supported Image File Formats

    • Abberior Inspector (.obf, .msr)
    • AmiraMesh (*.am)
    • Aperio SVS (*.svs)
    • arivis Single Image Stack 3 (*.sis)
    • BigDataViewer file format (*.xml)
    • CompuServe GIF (*.gif, *.giff)
    • DeltaVision image file (*.dv)
    • DICOM Directory (*.dicomdir, *.DICOMDIR)
    • DICOM Image (*.dcm)
    • Fiji/ImageJ-TIFF (*.tif, *.tiff
    • GE InCell (*.xdce)
    • Hamamatsu tiff-like file format (*.ndpi)
    • High Dynamic Range Image (*.hdr)
    • ICS 1.0/2.0 file format (*.ics, *.ibs)
    • Imaris IMS (*.ims)
    • Inspector (*.obf/*.msr)
    • JPEG/JFIF (*.jpg, *.jpeg, *.jif, *.jfif, *.j, *.jpe)
    • JPEG-2000 (*.jp2, *.j2k, *.j2c)
    • Leica Image File Format (*.lei,*.lif)
    • Luxendo images (saved as BigDataViewer *.xml)
    • Metamorph STK (*.stk)
    • Mirax SliceAC file format (*.mrxs)
    • Molecular Devices (GE IN Carta)
    • Neuroimaging Informatics Technology Initiative Image File Format (*.hdr, *.nii, *.nii.gz)
    • Nikon ND2 files (*.nd2)
    • Olympus file format (*.oir, *.oib, *.oif)
    • Olympus Media Handler (*.vsi)
    • OME-TIFF (*.tif, *.tiff)
    • OME-TIFF/FEI (*.tif, *.tiff)
    • OME-TIFF/LaVision (*.tif, *.tiff)
    • Perking Elmer PE (standard PE format, .qptiff Columbus metadata)
    • Portable Network Graphics (*.png)
    • Slidebook (.sld) Media Handler
    • TIFF Tagged Image (*.tif, *.tim, *.tiff)
    • TillVision file formats (*.rbinf, *.ini)
    • TrakEM2 Image file format (trakem2.xml, *.xml)
    • VGI/VOL Media Handler
    • VG Studio Max (*.vgl)
    • VG Studio Images VOL Media Handler (*.vol, *.vgi)
    • Virtual Microscopy Specimen file format (*.vms, *.vmu)
    • Windows Bitmap (*.bmp, *.rle, *.vga, *.rl4, *.rl8, *.sys)
    • Zeiss Axiovision ZVI (*.zvi)
    • Zeiss CZI/ZISRAW (*.czi, *.zisraw)
    • Zeiss LSM-tiff (*.lsm)
    • Yokogawa CV (*.mlf)
    • Yokogawa CPf (*.mmd)

Downloads

    • Preview image of ZEISS arivis

      ZEISS arivis

      Any Image Size, Many Formats, AI-Powered.

      19 MB
      Download
    • Preview image of ZEISS arivis

      ZEISS arivis

      Software Maintenance Agreement Enhanced Image Analysis Productivity

      787 KB
      Download
    • Preview image of ZEISS arivis Pro

      ZEISS arivis Pro

      Powerful, flexible software solution for demanding image analysis and visualization tasks

      4 MB
      Download
    • Preview image of Data Mining of Electron Microscopy Images

      Data Mining of Electron Microscopy Images

      Image Analysis Workflow for ZEISS arivis Hub & Pro

      1 MB
      Download
    • Preview image of Overcoming 3D Visualization Artifacts in Deep Learning-Based Bioimage Analysis

      Overcoming 3D Visualization Artifacts in Deep Learning-Based Bioimage Analysis

      1 MB
      Download
    • Preview image of Selected Life Science Research Studies with ZEISS arivis Pro

      Selected Life Science Research Studies with ZEISS arivis Pro

      1 MB
      Download

Visit the ZEISS Download Center for available translations and further manuals.

Talk to an Expert

To learn more about ZEISS arivis Pro microscopy image analysis software, please contact us. You can fill and send this form and one of our professional representatives will be happy to assist you.

Form is loading...

Please enter a valid email address and avoid typing errors. The data entered will be passed on to Carl Zeiss Microscopy Software Center Rostock GmbH, which is part of the ZEISS Group. An arivis specialist will contact you shortly.

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