NCTracer (Neural Circuit Tracer) is open-source software for automated and manual tracing of neurites from single 3D stacks of light microscopy images.

Installation and System Requirements

NCTracer 4.0 works with Windows 7-10 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 NCTracer_4_0_Setup.exe (~500Mb, updated May 09, 2014), right-click on the 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). Make sure that no other versions of these components are installed on your computer. To run NCTracer double-click on the NCTracer icon created on your desktop.

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 other versions of MATLAB Compiler Runtime and Java 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 the “mclmcr.dll” file was copied to the “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