arivis Scientific Image Analysis

ZEISS arivis Pro

new arivis pro


Automated End-to-End Image Analysis Pipelines

ZEISS arivis Pro is your modular image analysis software when working with multi-channel 2D, 3D, and 4D images of virtually unlimited size. With ZEISS arivis Pro (formerly Vision4D) it is easy to create automated end-to-end image analysis pipelines with just a few clicks. Use predefined pipelines for common use cases or create your own pipelines using the flexible click-and-play interface.

tick-iconHighly scalable computing, not dependent on local system resources 

tick-iconProcessing and quantifying any kind of multidimensional image data 

tick-iconCombining different operators for complex analysis 

tick-iconDenoising, AI-driven segmentation, filtering, thresholding and more

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Powerful scientific image analysis approach at your fingertips

Hardware and data-agnostic image analysis software

The ZEISS arivis Pro analysis strategy and iterative approach allow processing and segmentation of a small field of view, a 3D/4D subset, or the entire dataset. Analysis results can be viewed in synchronized split windows in 2D and 3D views simultaneously, which is particularly useful for densely packed structures and tracking experiments. The software's integrated Machine Learning/Deep Learning functionality (available as local training option or in the ZEISS arivis Cloud) allows for setting up an image segmentation and analysis pipeline with ease and without extensive knowledge of AI analysis methods. 

Analyze complex and challenging samples with a few clicks. No matter the source and format of the image, the arivis scientific image analysis platform is designed to easily process and analyze it. Our software tools are highly integrated and can benefit customers in academia, across industries and various applications, including biotech, pharma, life science and material science.

Supported File Formats >

  • Immediate visualization, annotation and analysis on workstations and notebooks in 2D, 3D and 4D, regardless of image size
  • Advanced and easy-to-use image analysis tools with interactive preview options
  • Easy to set up and train integrated AI, Machine Learning or Deep Learning models for segmentation, image processing and object classification for quick, reliable and reproducible results 
  • Scalable and integrated pipelines that connect ZEN, ZEISS arivis Cloud (formerly APEER), MATLAB, Cellpose/Stardist, Python, and more
  • Distance measurements, compartmentalization and classification
  • Powerful analysis pipeline for 3D/4D image analysis (cell segmentation, tracking, tracing, annotation, quantitative measurement and statistics)
  • High resolution images and movies for rapid publication and awesome presentation of your research data
  • Get a new perspective of your sample with the immersive virtual reality experience using ZEISS arivis Pro VR toolkit
  • Scale your image analysis by using your pipeline in ZEISS arivis Hub 

ZEISS arivis Pro and ZEISS arivis Cloud for Volume Electron Microscopy

AI-assisted 3D Density Analysis of a HeLa cell, imaged with ZEISS FIB-SEM Technology 


Original datasets imaged with a ZEISS FIB-SEM instrument and kindly provided by Anna Steyer and Yannick Schwab, EMBL Heidelberg, Germany.


ZEISS arivis  Cloud was implemented to train neural networks that identify large organelles: mitochondria and the nucleus. Using the arivis AI toolkit on ZEISS arivis Cloud (formerly APEER), we manually annotated a subset of the instances of these cellular features and trained neural-network models that successfully predicted the remainder of the instances of cellular features within the FIB-SEM image volume. These AI-trained models were first used to infer mitochondria and the nucleus in ZEISS arivis Pro (formerly Vison4D). We then built automated analysis pipelines to filter and improve the initial inferences into usable 3D segments.

Overall, this work highlights how the deep learning approach, when combined with the powerful 3D tools of ZEISS arivis Pro, enables 3D segmentation and measurements within FIB-SEM image sets.

Optional Modules and Toolkits

arivis Pro VR Toolkit

Get a new perspective and experience your sample in a whole new dimention with the emersive virtual reality environment, using the arivis Pro VR toolkit.

  • New Voice control features allow for an unrestricted experience, freeing you from your mouse and keyboard. 
  • Improved tracking and proofreading features take your image analysis to the next level. When automatic algorithms meet their limitations, use Virtual Reality with arivis Pro VR toolkit (formerly VisionVR) to proofread and correct your automatically created results much more efficiently, and with increased accuracy.
  • Creating awesome videos and 3D renderings of your results has never been easier. Mark points of interest while "walking through" your sample and allow the software to do the rest. 
  • arivis Pro VR offers advanced visualization, collaboration and analysis.

Importing Labled Images

The arivis Pro Exchange Objects Module allows for easy interface and import of your specific workflows from a third-party or open source, such as FiJI, ImageJ or Ilastik. Import your workflow with a single step and visualize or further analyze your 3D objects with ZEISS arivis Pro.  Create high-quality renderings to publish your results. The 2D/3D split views allow interactive exploration of the results or interactive gating in scatter plots or timeline graphs.

Batch Analysis 

The arivis Pro Batch Analysis Module can be used for the unattended execution of a pre-configured analysis pipeline on a series of images or regions of interest. The pipeline is easily adapted and can be applied to multiple datasets. 

Automatic Neuron Tracing

Trace your Neurons with a new level of accuracy and speed

Automatic Neuron Tracing includes two established scientific methods to choose from.  Neuroscientists use this module to generate quick results even with large microscopy imaging data.

The state-of-the-art, integrated algorithms can save you precious time and effort when visualizing and tracing neuroscience datasets. The module offers compatibility and flexibility for a wide range of sample data and imaging modalities.

No matter if your research centers on confocal or light-sheet microscopy, single neurons or cleared tissue applications, Automatic Neuron Tracing includes a wide variety of the most relevant trace measurements. The easy-to-use, high-performance semi-automatic trace editing tool enables easy correction of trace paths even for difficult samples.

arivis Storyboard assists you with export of impressive cinema-quality animations of your results: Let your data speak for itself!

Waltz of the Neurons


 Automated 3D neuron tracing of neuronal tissue (mouse brain) with Vision4D 4.0 and ZEISS LSM 980 confocal microscope. Original 3D tissue volume dataset (45GB CZI, confocal fluorescence microscopy, single channel) kindly provided by Dr. Steffen Burgold, ZEISS RMS Customer Center Oberkochen, Germany. 

Hardware and Data-Agnostic, Scalable, Automated and Integrated

Import and save Import Image support does not depend on the source of your data. It enables users to work with multiple image modalities.  
strategic-business-unitsS 4D Viewer Visualize large-scale 3D/4D image stacks, multi-channel and multi-dimensional. Up to Terabyte data volumes.  
chart-statistics-key-figures Automated Pipeline The analysis pipeline is an intuitive, fast and flexible tool to automate your image analysis, tailoring it to your needs.  

Customers and Partners

Leading institutes and research organizations trust ZEISS arivis for scientific image analysis.

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