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Your powerful scientific imaging software

arivis Vision4D is your modular software for multi-channel 2D, 3D and 4D images of almost unlimited size, highly scalable and independent of local system resources. Many modern microscope systems such as high-speed confocal, light sheet, super-resolution, electron microscopy or X-ray instruments can produce huge amounts of imaging data. Handle your datasets without constraints and get your results in next to no time!

For quantification of 3D image data the arivis Analysis Pipeline offers a robust and flexible click-and-play solution for processing and quantification of any kind of multidimensional microscope image data. Start your image anaylsis today, even if you are not an image analysis expert or programmer. Using the flexible Analysis Pipeline novices can start with predefined workflows for common use cases, while experts have the flexibility to combine different operators for denoising, segmentation, filtering, and other analysis tasks in a clearly structured pipeline with an interactive preview. The analysis strategy and iterative approach of arivis Vision4D allows image processing and segmentation of a small field of view, a 3D/4D subset, or the complete data set.

Analysis results can be reviewed in synchronized split view windows in 2D and 3D view simultaneously, which is particularly helpful for densely packed structures and for tracking experiments. The integrated Machine Learning/Deep Learning functionality allows the segmentation of even difficult samples easily and without deep knowledge of AI analysis methods.

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 and integrated AI with Machine Learning for segmentation, image processing and object classification for quick and reliable results including Deep Learning solutions
  • Open, scalable and integrated workflows that connect ZEN, APEER, MATLAB and a multitude of Open Source platforms such as Stardist, Cellpose, ...
  • Distance measurements, compartmentalization and classification
  • Powerful Analysis Pipeline for 3D/4D image analysis (cell segmentation, tracking, tracing, annotation, quantitative measurement and statistics, etc)
  • Easy creation and export of 3D/4D high resolution images and movies for rapid  publication & perfect presentation of your research data
  • The Scientific Imaging Platform directly integrates with VisionVR for productive and immersive visualization and analysis in Virtual Reality, and VisionHub, the scalable solution for data management, storage and processing

Vision4D for 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.


APEER by ZEISS was implemented to train neural networks that identify large organelles: mitochondria and the nucleus. Using the APEER platform, we manually draw a subset of the instances of these cellular features and train neural-network models that successfully predict the remainder of the instances of cellular features within the FIB-SEM image volume. These APEER-trained models were first used to infer mitochondria and the nucleus in arivis Vison4D. We then built Vision4D analysis pipelines to filter and improve the initial inferences into usable 3D segments.

Overall, this work highlights how the APEER deep learning approach, when combined with the powerful 3D tools of Vision4D, enables 3D segmentation and measurements within FIB-SEM image sets.

Optional Modules

Tracking & Lineage Module

Tracking cells or sub-cellular particles in microscopy data can be challenging. The arivis
Vision4D Tracking & Lineage Module allows the tracking of objects throughout time series in both 2D or 3D image sets of any size. Vision4D offers an easy to use approach with full control and interactivity at all steps. Several automatic algorithms allow fast and reproducible tracking which can be readily applied to other data sets. When automatic algorithms meet their limitations, use Virtual Reality with VisionVR to proof read and correct your automatically created results much more efficiently than ever before.

Batch Analysis Module

The arivis Vision4D 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. Analysis pipelines created in the arivis Analysis Module can easily be applied to multiple datasets. For routine workflows and inexperienced users, predefined Analysis Pipelines can be used and adapted easily.

Exchange Objects from Open Source and Third Party

The arivis Vision4D Exchange Objects Module allows to easily interface with your specific workflows whenever you are using segmentation functions in open source, such as FiJI, ImageJ or Ilastik. Import these results with a single step and visualize or further analyze your 3D objects to measure e.g. volumes or count vesicles within cells or ROIs. Create high quality renderings for publications from segmentation results from other programs. The 2D/3D split views allow interactive exploration of the results in 3D with feature-based color coding or interactive gating in scatter plots or time line graphs.

Volume Fusion

This tool allows to fuse two image sets at any arbitrary angle in 3D. You can rotate and translate one image set against another image set and merge them to create a fused volume for further processing, rendering or analysis. Settings for the rotation, translation and scaling of the volumes can easily be configured using landmark registration or by rotating a surface extracted from the moving volume directly in the 4D viewer. The ability to merge volumes into new channels or to blend them into the existing volume data adds a high level of flexibility for further processing workflows.

Automatic Neuron Tracing

Automatic Neuron Tracing vor Vision4D 4.0 gives you the option to choose between two published state-of-the-art algorithms to facilitate automated analysis of your imaging data with a maximum of compatibility for your specific samples and imaging modalities. No matter if your research centers on confocal or light-sheet microscopy, single neurons or cleared tissue applications, small or large datasets: the new module gives you the flexibility to adapt the automatic analysis for better, faster results that you can trust. Automatic Neuron Tracing includes a wide variety of the most relevant trace measurements with convenient export options and an easy-to-use high-performance semi-automatic trace editing tool to correct trace paths for difficult samples. 

Automatic Neuron Tracing

Automatic Neuron Tracing includes two established scientific methods to choose from, giving Neuroscientists faster-than-ever results even with large microscopy imaging data.

The integrated algorithms can save you precious time and effort when visualizing and tracing neuroscience datasets while at the same time ensuring flexibility for a wide range of sample data and imaging modalities.

arivis Storyboard assists you with export of impressive cinema-quality animations and visualizations with resolutions of up to 4k60: 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. 

Waltz of the Neurons


Vision4D: Open, scalable, integrated

Import arivis Vision4D image support is vendor-independent and enables users to work with multimodality data  
4D Viewer Visualize large-scale 3D/4D image stacks, multi-channel and multi-dimensional, up to Terabyte volumes  
Analysis Pipeline The Analysis Pipeline is an intuitive, fast and flexible tool to tailor the processing of image data to your needs  


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