Software for 3D Neuron Tracing | Bitplane

Innovative 3D Neuron Tracing with Imaris

The Imaris for Neuroscientists package is the perfect combination of tools for researchers working in various neuroscience disciplines. Imaris enriches advanced 3D/4D visualization and analysis methods with Filament Tracer - best in class software for an automated detection of neurons including spines and other filamentous structures in 2D/3D or 4D datasets, measurements, object tracking, plotting, group comparisons with statistical tests and two-way interface for customization in Matlab, Java or Python. Neuroscientists will also appreciate that Imaris has the ability to simultaneously visualise multiple 2D, 3D or 4D images with differing spatial or temporal dimensions and resolutions.

Tracing neurons and detection of cells and structures

Microscopy image analysis requires precise detection of multiple biological structures based on the initial signal saved as an image data. Object detection in Imaris will be quick and easy as users are guided within a wizard driven interface to create perfect models of their data. With our patented Torch™ tool and several performance improvements tracing neurons with Autopath or Autodepth in dense and thick samples is very efficient and becomes a unique experience.

Automatic Tracing
Object Detection
Spine Detection

Automatic Tracing

Automatic neuron tracing is guided within the wizard based interface – starting point and seed points along the filament are detected with just few mouse clicks.

  • Dedicated algorithms available for trees without loops or structures which may contain loops.
  • Adjust multiple parameters to ensure the best possible detection quality: amend automatically calculated threshold, add/delete start or end points of the filament.
  • Segmenting images even with sub-optimal quality (e.g. overall low signal to noise ratio and/or in the presence of high intensity (non-filament) points in the background).
  • All dendritic spines along the filament and creates a new class of objects.

Visualization and animation export

Imaris provides a complete set of features for visualization of multi-channel microscopy datasets from static 2D images to 3D time series regardless their size and format. Using Imaris for Neuroscientists users can:

  • Organize and manage full experiments including images and data analysis in Imaris Arena.
  • Use premier 3D/4D volume rendering modes: (MIP, Blend Projection, Shadow Rendering, Normal Shading)
  • Benefit from Imaris high performance IMS file format which guarantees smooth navigation even in very large 3D datasets (TB range).
  • Combine volume rendering, object representation, clipping planes and cross-section slices.
  • Make high quality snapshots ready to be used in publications in Snapshot Tool.
  • Easily make animations which include volume rendering, detected objects, annotations, object motion by adding several frames of interest in a Key Frame Animation Tool

Statistics and measurements

After segmenting the image data Imaris calculates a wide range of statistics for all detected objects: Filaments, Surfaces and Spots. All values can be used for color coding, plotted inside Imaris (using Vantage plots) or exported in an .csv or .xls file format. Parameters presented below are the most common statistic types needed by biologists. Imaris reports many more.


Mean Diameter
Branching Angle
Spine Density


Dendrite Branch Points
Dendrite Terminal Points
Sholl Intersections
Spine Terminal Points
Dendrite Branch Level


Mean Diameter
Terminal Point Diameter


Position (x, y, z)
Number (counting objects)

Further benefits of Imaris for Neuroscientists

This package is about much more than just tracing. With the inclusion of various Imaris modules, you can experience complete analysis freedom during your experiments.

Plotting and Comparison
Tracking Algorithms
Open-source Coding

Plotting and Data Comparison


Imaris Vantage plotting tool enables to visualize segmented objects on multi-variate scatterplots to discover hidden relationships between object statistics.

  • Up to 5 variates represented on xyz axes, size and color) or create a gallery of all detected objects (like spines or dendrites) to compare their shapes.
  • Two way interaction between original image and the plot: when the group of objects selected on the plot, it’s also highlighted on the original image.
  • Easily compare chosen statistics between your control and experimental groups on uni- or multi-variate scatterplots.
  • Test statistical hypotheses using: t-Test F-test, Kolmogorov-Smirnov, Wilcoxon.
  • All created plots are ready to use in papers and presentations - you can export them with Snapshot.

Additional Resources

The Imaris Learning Center hosts a wide range of tutorial videos, how-to articles and webinars to guide you through the many features of Imaris. We have provided some links below which will get you started on some of our most recent developments.

Imaris Stitcher

Accurate and precise stitching of multiple tiles in XYZ is now possible with our big data capable Imaris Stitcher. Simply load 2D, 3D or 4D tiles for stitching and the software will detect their stage coordinates.


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