Neuron Tracing & Trace Editing

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Automatic Tracing for Faster Results

Neuron Tracing in microscopy volume imaging data can be challenging and laborious. The Automatic Neuron Tracing module allows analysis of even complex structural networks in both 2D or 3D multichannel image sets of virtually any size (tested with 100s of GBs). The integration of two modern, published methods and state-of-the-art algorithms offers an easy-to-use approach with full flexibility and interactivity at all steps.

The novel software architecture and algorithms of the arivis Scientific Image Analysis Platform deliver top performance in tracing applications for various imaging modalities in light microscopy. Combined with our best-in-class Machine Learning segmentation, automatic tracing and trace editing of multidimensional data sets becomes an easy task, without the need to be an expert in bioinformatics. arivis Vision4D allows you to create expert results and meaningful output data for any kind of tracing data sets. The new semi-automatic trace editing tool creates a neuron trace or branch interactively by drawing in the viewer with automatic detection of the path. And the unique arivis VisionVR virtual reality solution gives you superior productivity when proofreading and correcting your automatically created results.

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Fast and Reproducible Tracing

Several parameters and state-of-the-art algorithms allow fast and reproducible tracing:

  • Choose between two published state-of-the-art algorithms
  • Maximum of compatibility for your specific samples and imaging modalities
  • Wide variety of the most relevant trace measurements with convenient export options
  • Easy-to-use high-performance semi-automatic trace editing tool to correct trace paths for difficult samples

Automatic Neuron Tracing with Complex Structural Tissue

"Forest of 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.                   


  • Module with two state-of-the-art published & peer reviewed algorithms
  • For any imaging technology (confocal, widefield, light-sheet microscopy etc), can adapt to different image qualities (varying background, local contrast differences)
  • Allows processing of larger images
  • Multi-threaded processing
  • Suitable for neurons with / without cell bodies
  • Fast and efficient editing of automatic Tracing results if needed
  • Semi-automatic Trace tools for easy editing with automatic trace detection
  • Pre-configured Measurements include:
    • Total length of all sections or path, Total volume
    • # of Branch Points, # of Terminals
    • Branch Level and Depth
    • Section Diameter Statistics
    • Terminal Section Length
    • Tortuosity  
    • …  and many more!

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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