Importing labelled images from Open Source

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The most flexible way to import & export imaging data & results

With arivis you can now integrate all tasks of image visualization and analysis of multidimensional microscopy imaging data of any size in a single software package.

The Open Source community offers many special functionalities and regularly adds new ones to the research community. On the other hand many users prefer a commercial, robust and fully supported image analysis platform with a unified UI that covers all aspects of image processing, analysis and visualization of results via desktop workstation, cloud computing or Virtual Reality. Therefore an easy transition between open source/third party packages and our arivis Scientific Imaging Platform is essential.

With the Vision4D Exchange Objects with Open Source module we offer an integrated solution to imaging facilities and PIs to connect with open source workflows as well as with any other software which is capable of exporting/importing labelled images. Easily interface with your specific workflows whenever you are using segmentation functions with open source packages such as Fiji, ImageJ, Ilastik, Python or with commercial solutions such as MATLAB or ZEN/APEER software by ZEISS Microscopy.

No programming knowledge needed - Vision4D adapts to your requirements and workflows!

Importing Labelled Images Workflow


Acquire Acquire your raw microscopy data

Perform segmentation with your preferred scientific open source or commercial package

Export Export segments as labeled images
Analyze Convert labeled images into 3D objects to create 3D movies and enable further analysis 

Use Machine Learning-based segmentation in whole mouse brain light sheet data

Constanze Depp from the Max Planck Institute of Experimental Medicine is presenting a whole brain quantification of amyloid plaque load using Machine Learning in arivis Vision4D.
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Vision4D Video Tutorials

Import Objects from Open Source

Import from open source or other software into Vision4D and create impressive movies

Import resulting objects e.g. from Fiji or any other software in a single step into Vision4D and visualize the segmentation in 3D to create impressive movies with our arivis storyboard. This is a combined workflow using Ilastik autocontext, 3D segmentation using ImageJ-Matlab. 

Image courtesy of Dr. Carlo Beretta, Livia Asan, Dr. Johannes Knabbe and Prof. Dr. Thomas Kuner, Department of Functional Neuroanatomy, Heidelberg University

Explore & edit resulting objects from open source and Vision4D in arivis VisionVR

Import resulting objects e.g. from Fiji or any other software in a single step into Vision4D, then explore and edit the results from open source in immersive Virtual Reality with VisionVR. This is a combined workflow using Ilastik auto context, 3D segmentation using ImageJ-Matlab.

Image courtesy of Dr. Carlo Beretta, Livia Asan, Dr. Johannes Knabbe and Prof. Dr. Thomas Kuner, Department of Functional Neuroanatomy, Heidelberg University

Full Integration in arivis Vision4D

The one-step import and export of objects allows to add more functionality from Open Source or other microscopy software packages to the proven 3D visualization and analysis functionality of your arivis Scientific Imaging Platform, making it the most flexible solution on the market. No specialized coding/programming skills required!

Your benefits:

  • An easy workflow integrating functionality offered by other software packages
  • Create high quality movie renderings for your publications 
  • Visualize results in synchronized 2D/3D split views
  • Visualize results with feature-based color coding or interactive gating in scatter plots or time line graphs
  • Explore and further edit your results with VisionVR in Virtual Reality
  • Analyze your 3D objects to measure, e.g. volumes or count vesicles within cells or arbitrary 3D ROIs
  • Add further processing such as Tracking and Grouping with our flexible arivis Pipeline

arivis Vision4D works for several different multi-dimensional images from many modalities in microscopy:

  • Fluorescence Microscopy
  • Superresolution Microscopy
  • Transmission Light or Label Free Microscopy
  • Confocal Microscopy
  • Light Sheet Microscopy
  • Electron Microscopy (2D and 3D)
  • X-ray Microscopy
  • CT and MRT images


 CZI, TIFF, JPG, PNG, TXM and all Bio-Formats compatible images including third-party vendor-specific file formats enabled through SIS Converter.

The arivis Imaging Platform

The arivis Imaging Platform is a flexible computing universe for Imaging Science that scales, parallelizes, integrates and connects all imaging workflows, sparking organization-wide image data proficiency and efficiency at all levels. The integrated toolsets take care of everything from the file storage format to user and project-specific computations to reporting. The computational and management hubs that comprise the platform connect your datasets and take care of your central imaging databases and can expose data assets - including raw data and specified portions of raw data - to Machine Learning and AI routines.


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