Neural Circuit Tracer

Neural Circuit Tracer (NCTracer) is open source software for automated and manual tracing of neurites from light microscopy stacks of images.

Installation and System Requirements

NCTracer 4.0 is developed for Windows 7 and 8, 64-bit operating systems and requires a minimum of 4 GB of RAM. This version does not run on Mac or Linux OS.

To install NCTracer 4.0 download (~500Mb, updated May 09, 2014) and extract its components. Right-click on Setup.exe file and run it as Administrator. This will install four components: Java (jre-7-windows-x64), Java3D (java3d-1_5_2-windows-amd64), MatLab Runtime Compiler (MCR_R2013a_win64), and NCTracer (NCT_4_0). It is recommended that you install all four components even if some of these components are already present in your computer. To run NCTracer double-click on the NCTracer icon created on your desktop.

User Guide

NCTracer 4.0 user guide

Troubleshooting Instructions

If you are unable to launch NCTracer 4.0, or unable to load/open an image stack, try the following steps:

1. Uninstall all versions of the NCTracer, Java(TM) 7 64-bit, Java 3D 1.5.2, and MATLAB Compiler Runtime 8.1.
2. Make sure you don’t have any older version of MATLAB Compiler Runtime installed.
3. Restart the computer.
4. Re-install NCTracer 4.0 with “Run as Administrator”. Make sure to install all the components.
5. Make sure that “mclmcr.dll” file was copied to “C:\Program Files\MATLAB\MATLAB Compiler Runtime\v81\bin\win64” folder.
6. Go to Start and right-click on Computer. Go to Properties->Advanced System Settings -> Environment Variables. Double click on Path in System Variables and make sure that it contains:
C:\Program Files\Java\Java3D\1.5.2\bin
C:\Program Files\Java\jre7\bin
C:\Program Files\MATLAB\MATLAB Compiler Runtime\v81\bin\win64
C:\Program Files\MATLAB\MATLAB Compiler Runtime\v81\runtime\win64


Online Training demo is coming soon.

  • Contact Information:

    Prof. Armen Stepanyants
    Department of Physics
    Northeastern University
    110 Forsyth St.
    Boston, MA 02115
    Tel: (617) 373-2944
    Fax: (617) 373-2943

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