Software & Protocols

The following posts contain open source code and various other software developed in the Murphy Lab. If any of the software is used, please cite the relevant paper or author(s); where applicable, citations in AMA style have been provided on the page for your convenience.


Software and websites used in the lab:

  • Blender, open source 3D animation
  • Inkscape, open source vector graphics software for figure making
  • Fiji, a distribution of ImageJ that includes plugins for scientific image analysis
  • Codeacademy, programming tutorials


You may use software of this site that is linked or described on this page for any personal, commercial or educational purpose, including installing it on as many different computers as you wish. You may also copy, distribute, modify, and/or sell it under the terms of the GNU General Public License (GPL) as published by the Free Software Foundation – either version 2 of the License, or (at your option) any later version. In granting you this right, the GPL requires that the source code you distribute is itself available under the GPL. If you have questions, please contact us.



IO and VSD Signal Processor
Plugin for ImageJ for analysis of Intrinsic Optical Signal (IOS) or Voltage Sensitive Dye (VSD) fluorescence signal in imaging data.

Dispose All Windows: ImageJ plugin
This ImageJ plugin closes all image windows and non-image windows as selected by the user.

Interpolate NaN
Small plugin forĀ ImageJĀ to interpolate pixels with value "NaN" and "infinity" in images or image stacks.

BlebQuant: Automated and quantitative analysis of blebbed dendrites
BlebQuant is developed for automated detection and quantification of blebbing.

Neurophotonics tutorial on making connectivity diagrams from Channelrhodopsin-2 stimulated data
This package of sample data and MATLAB codes will process, filter, and average raw voltage sensitive dye images, as well as generate a comprehensive connectivity matrix and a network diagram.

Automated homecages
Download the code and 3D printer files for the automated homecages used in the Murphy Lab.

Software developed RFID tagging of mice Python
Download the Python scripts as a zip file.

Software developed for mesoscale brain mapping, open source Python with GUI
GitHub repository for the Mesoscale Brain Explorer (MBE).

Software and hardware for automated mouse tapered beam test
Download the Python code and 3D printer files for the automated mouse tapered beam test developed in the Murphy Lab.

Mouse homecage motor task hardware description
Images showing the motor task hardware in the mouse homecages used in the Murphy Lab.