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neuroGit - A suite of Matlab© packages for visual neuroscience.

This software is free to download and use under a public license. If used, please cite: Caudill M.S., neurogit, (2013), GitHub repository,



StimGen is a visual stimulation package capable of drawing complex visual stimuli to a set of monitors with millisecond timing accuracy. The package utilizes Matlab's abstract structure array data type to store all the parameters of a visual stimulus. The structure arrays can be tagged with a user specified name to facilitate data processing.

Further, the package supports parallel port triggering on the following computer architectures: 32-bit and 64-bit Windows XP and Windows 7. This allows users to initiate a cascade of data acquistions sequences with millisecond timing accuracy. A range of possible stimuli are provided in the stimGenStimuli directory. These stimuli are modular and feature expemplary code annotation to aid developers in creating new stimuli.



Ephys is an electrophysiology analysis package for cell-attached and whole-cell recordings from single cells recorded in-vivo. It supports data collected from multiple hardware channels on Matlab 'DAQ' and Axoclamp Digidata devices. The software walks the user through the following processing stages for each hardware channel:

  • Data Selection
  • Data Visualization
  • IIR Filtering
  • Butterworth
  • Chebyshev
  • Elliptic
  • Spike detection
  • Results

Ephys seamlessly integrates with the stimGen visual stimulation software. The stimulus, recorded signals, and analysis results are paired and stored using Matlab's structure array data type. The multi-channel support feature allows users to greatly expand Ephys processing capabilitiesby allowing users to sort electrophysiology trials according to various behavior and physiology signals.


CAIMG is an extensive package for calcium indicator response analysis. Two guis and supporting helper functions seamlessly integrate visual stimuli from the stimGen package with imaging stacks collected using two-photon microscopy running scan-image software. The guis and the functionality they provide are:


  • Data Selection and Visualization
  • Autodetection of missed triggers
  • Motion Correction
  • Supports separating optogenetic & control trials
  • Supports non-imaging data collected from Matlab 'DAQ' or Axoclamp hardware channels.


  • Data Visualization including video playback
  • Region of interest (ROI) selection
  • Tagging of neuron type
  • Fluoresence calculations with neuropil subtraction
  • Support for separating calculations of optogenetic and control trials
  • Supports separating trials based on behavior and physiology from hardware signals

CaImg utilizes Matlab's abstract map container object to store all the stimulus information and the signals for each individual roi. This container object makes it easy to carry out further calculations on the fluoresence signals from each roi. The package includes numerous scripts that demonstrate the interaction with the signal map object.

Intrinsic Imaging

A package for analyzing hemodynamic flow in response to stimuli. Currently supports only tiff format images.


  • Windows XP and greater.
  • Matlab version 2013a or greater.


A git repository for visual stimulus delivery and data analysis of imaging and electrophysiology data



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