arivis Scientific Image Analysis

Neuron Tracing and 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. ZEISS arivis Pro (formerly 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 ZEISS arivis Pro VR (formerly VisionVR) virtual reality solution gives you superior productivity when proofreading and correcting your automatically created results.



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 ZEISS arivis Pro (formelry 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.



Automatic Neuron Tracing

Improved Neuron Tracing Module
  • Module with two state-of-the-art published- and 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 proofing and editing of automatic tracing results
  • 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 Image Analysis Platform

The arivis Scientific Image Analysis Platform is a flexible computing universe that scales, parallelizes, and streamlines all imaging workflows. With arivis' easy sharing functions your organization can enjoy data proficiency and efficiency at new levels. arivis includes integrated toolsets that handle everything, from file storage format to project and user-specific computations, to reporting. The platform's hubs connect datasets and manage central imaging databases and raw data exposure, while also enabling Machine Learning and AI routines.

placeholder40px ZEISS arivis Hub A nucleus of computational activity and collaboration at scale. ZEISS arivis Hub enables design and execution of large-scale experiments that produce results from images, whether datasets are already stored or are actively being produced. Mass quantities of microscopy data are onboarded and processed by a virtual team of computational workers. Smartly utilize processing cores in servers or workstations with maximum possible speed.  
placeholder40px ZEISS arivis Pro

Extract results from your scientific images with ZEISS arivis Pro. Make the most of hardware power adjustments and smooth interactivity on microscopy datasets of virtually unlimited size. The software unites multiple tools for visualization and advanced analysis into one easy-to-learn user environment for high productivity. Extend your possibilities with the Python coding feature and a multitude of supported libraries and APIs. Optional Virtual Reality interface.

placeholder40px ZEISS arivis Cloud Train Deep Learning models to automate your image analysis in ZEISS arivis Cloud (formerly APEER). Whether you use standard pipelines for routine tasks or create your own application, you can power your research with AI with just a few clicks. You can train your own model or alternatively, select a pre-defined pipeline and use a previously trained model on your images. The AI-trained models can be used with other ZEISS software products. Read More

Our Team is Happy to Help you

We would love to hear from you and learn about your neuron tracing needs.