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.

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Sub cellular analysis based in AI model of FIB SEM image — 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 — 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 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). — Courtesy of Dr. Steffen Burgold, ZEISS RMS Customer Center Oberkochen, Germany.

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.

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.

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

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)

Supported image file formats

Advanced Image Analysis Made Even Easier with ZEISS arivis Pro 4.3

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

Download the life science case study
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
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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

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.

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

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 background 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)
Improved: 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 slightly 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 assignment)
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

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)
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)
Download SIS Converter

Downloads

ZEISS arivis product family information

ZEISS arivis software solutions for advanced image analysis

6 MB

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ZEISS arivis

Software Maintenance Agreement Enhanced Image Analysis Productivity

787 KB

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ZEISS arivis Pro

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

4 MB

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ZEISS Solutions for Semiconductor Development, Manufacturing, and Analysis

Accelerating Digital Transformation and Innovation for Semiconductor Electronics

13 MB

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Data Mining of Electron Microscopy Images

Image Analysis Workflow for ZEISS arivis Hub & Pro

1 MB

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

1 MB

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Selected Life Science Research Studies with ZEISS arivis Pro

1 MB

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

ZEISS arivis Pro

Your Solution for Advanced Image Analysis and Visualization