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
  • Boost your research with AI with no coding
  • 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.

Flexible, End-to-End Image Analysis Pipelines

ZEISS arivis Pro empowers you to automate image analysis and visualization pipelines. 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.

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, even for complex tasks. Annotate slices in your Z-stack to train your model 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 automated pipeline. 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

Complex disease 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.

Octopus sample visualized and viewed in a VR environment with voice control.
Octopus sample visualized and viewed in a VR environment with voice control.

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.

  • ZEISS arivis Software Puts User Customization at the Forefront of Microscopy Image Analysis

    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
  • Sample of Arabidopsis thaliana cryo-volume electron microscopy (Cryo-vEM) provided by York-Dieter Stierhof, Tübingen University.

    Summary of changes in arivis Vision4D 4.1.2 released 16 November 2023

    Cellpose Segmenter:

    • Improved: better memory checks to avoid internal errors
    • Improved: more clear error and warnings
    • Improved: better description of the available pre-trained models in the help
    • Change: perform planewise is enabled by default now
    • Fix: handling of results for time points other than the first one (in combination with voxel filters)
    • Fix: normalization for data with bias in min intensity value
    • Fix: other small fixes for the Cellpose Segmenter

    Import:

    • Improved: importing channel names for XDCE data
    • Fix: import problems for some ND2 time series

    General:

    • Improved: faster free consumed license after quit of the application
  • Neurospheres detected with pre-trained cellpose ai model.

    Neurospheres detected with pre-trained cellpose ai model.

    Neurospheres detected with pre-trained cellpose ai model.

    Neurospheres detected with pre-trained cellpose ai model.

    Neurospheres detected with pre-trained cellpose ai model.

    Summary of changes in arivis Vision4D 4.1.1
    Released 25 July 2023

    New & Noteworthy:

    • Cellpose Segmenter - directly import pre-trained Cellpose models for easy and fast segmentation in the Analysis Pipeline

    Analysis:

    • New: native Cellpose Segmenter analysis operation (no Python needed)
    • New: export a created model from Deep Learning Trainer as CZANN
    • Improved: Deep Learning - better compatibility with N2V models from ZEISS ZEN
    • Improved: Allow Holes option is on by default for the DL Segmenter
    • Improved: better conflict validation when renaming DL trainings
    • Fix: rare cases where positions of tracks after scaled analysis are incorrect
    • Fix: potential wrong segment reference for cell body in a trace

    4D Viewer:

    • Improved: auto zoom when double clicking an object is more usable in 4D Viewer
    • Fix: sometimes traces (in cone display style) were not selectable in 4D Viewer

    General:

    • New: provide a description and an offline download for optional components in the installer
    • Fix: improved compatibility for DeltaVision DV import
    • Fix: What's New opens after an update more reliable
    • Fix: installer makes sure that no files from former Vision4D versions are left in the installation folder
    • Additional small fixes and improvements in the arivis_dl library
  • DL training operation

    DL training operation

    DL training operation

    DL training operation

    DL training operation

    Summary of changes in arivis Vision4D 4.1
    Released 27 March 2023

    New & Noteworthy:

    • New optional module: arivis AI toolkit features a complete Deep Learning workflow right in Vision4D - annotate, train & inference
    • Various improvements in the tracing workflow
    • Wellplate Editor to manually assign imagesets to wells or fields of a well

    arivis AI Toolkit:

    • New: Optional module arivis AI toolkit
    • New: Deep Learning Trainer panel to setup and train a DL model
    • New: use the Draw Tool to draw segments to annotate regions for classes
    • New: utilizing of sparse annotations to overcome the need to draw on every pixel
    • New: drawn objects are sorted by class order - pixels are assigned to the topmost one (no need to cut out overlaps)
    • New: add and reuse existing segments for class definition
    • New: automatic clustering based on annotated backgound possible
    • New: run and monitor the DL training process right from Vision4D
    • New: directly open the trained DL model in the Analysis Pipeline for inference
    • New: export the trained DL model as ONNX
    • New: additional installer package to setup a whole DL Python environment

    Tools:

    • New: Draw Tool has a context menu and better keyboard shortcut support
    • New: Draw Tool is aware of the DL Training panel
    • New: Draw Tool allows to change class to draw by shortcut or context menu (in DL Trainer mode)
    • IIproved: Trace Tool - connect to a cell body segment
    • Improved: Trace Tool - optimized remove branch
    • Improved: 'unable to connect' messages in the Trace Tool are more understandable

    Analysis:

    • New: 'Neuron Tracer' (from the Segmentation category) has been renamed to 'Neurite Tracer'
    • New: 'Neuron Tracer (from Cell Body)' has been renamed to 'Neuron Tracer'
    • New: Neuron Tracer preview shows all parts in the same color
    • New: Neuron Tracer preview shows the filtered parts slighly dimmed (instead of hiding them completely)
    • Improved: parameter labels in the Neuron Tracer are more precise
    • Improved: default threshold value and threshold warnings in the Neuron Tracer
    • Improved: tooltips in the Neuron Tracer
    • Fix: if the tracking operation had a lot of results, it could happen that the last tracks were not displayed
    • Fix: prevent the creation of (almost) empty traces in the Neuron Tracer
    • Fix: ensure that a preview progress label is always displayed immediately

    Visualization:

    • New: display of starting points can be turned off for traces
    • Improved: optimized cone generation for traces in 4D Viewer
    • Improved: fallback to line based visualization if cones for traces would exceed memory
    • Improved: remember last used Z-Projection value for trace visualization in 2D
    • Fix: minor problem with RGB Projection in 4D Viewer

    Data Handling:

    • New: Wellplate Editor to manually assign imagesets to wells or fields of a well
    • New: semi-automatic assign imagesets to well or field positions based on the name of the imageset (in the Wellplate Editor)
    • New: additional import scenario to import wells as imagesets and open the Wellplate Editor afterwards (for manual assignemnt)
    • Fix: some LaVision data could not be imported correctly for TileSorter
    • Fix: problems with some CZI if imported for TileSorter

    General:

    • New: Predictive Analytics service as optional install
    • New: gRPC service connector
    • New: ZenBridge is able to work with gRPC service connector (optionally)
    • Improved: included Sentinel driver and HASP Lib have been upgraded to version 8.5
    • Fix: sort order in field selector of Navigator (for wellplate data)
    • Fix: rare crash in the Transform Surface dialog
    • Additional minor fixes and improvements

Supported Image File Formats

    • Abberior Imspector (.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)
    • Imspector (*.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

    • ZEISS arivis Pro

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

      File size: 1 MB

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.

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