Category: Software


Ian Dublon, former postdoctoral researcher at the


The program itself is relatively simple and originated out of the real need to rapidly appraise 2d calcium imaging datasets and the frustrations with existing acquisition software relying exclusively on defined regions of interest (ROIs). There is of course nothing wrong with ROIs but it is useful to rapidly appraise the the whole matrix. It really depends on the biological question being asked.

At its most simple, when you open a stacked Tiff, scintillate uses MATLAB’s imabsdiff to look at the absolute difference across the image matrix for successive frames in the stack. Several other more powerful tools, including background pre-stimulus subtraction and ICA (using the excellent FastICA) are provided to help the user ascertain the value of the studied preparation. This helps to confirm and pinpoint areas of signal change, allowing the imager to make adjustments to image acquisition parameters or simply to start afresh.

Written as a GUI in MATLAB and with source and GUIDE files provided alongside a getting started manual, it is designed both for image acquisition people and for MATLAB coders. If the compiler toolbox is present its possible to package a version of scintillate that will run without a MATLAB install present, making it ideal for running on the image acquisition workstation. Simply provide it with an acquired stacked tiff and within three or so clicks and no command line syntax you are ready to go.

Code is hosted at GitHub here: and scintillate uses some freely available 3rd party code which is gladly acknowledged throughout. Scintillate is not designed to replace traditional analysis methods but rather to provide a means of open-source rapid evaluation during the pre-processing stage. It is hoped that by hosting it on GitHub it may be developed further and thus adjusted to suit each persons individual imaging needs.

Oculomatic Eye-Tracking

Jan Zimmerman, a postdoc fellow in the Glimcher Lab at New York University has shared the following about Oculomatic:

captureVideo-based noninvasive eye trackers are an extremely useful tool for many areas of research. Many open-source eye trackers are available but current open-source systems are not designed to track eye movements with the temporal resolution required to investigate the mechanisms of oculomotor behavior. Commercial systems are available but employ closed source hardware and software and are relatively expensive therefore limiting wide-spread use.

Here we present Oculomatic, an open-source software and modular hardware solution to eye tracking for use in humans and non-human primates. Our fully modular hardware implementation relies on machine vision USB3 camera systems paired with affordable lens options from the surveillance sector. Our cross platform software implementation (C++) relies on openFrameworks as well as openCV and uses binary image statistics (following Green’s theorem) to compute pupil location and diameter. Oculomatic makes use of data acquisition devices to output eye position as calibrated analog voltages for direct integration into the electrophysiological acquisition chain.

Oculomatic features high temporal resolution (up to 600Hz), real-time eye tracking with high spatial accuracy (< 0.5°), and low system latency (< 1.8ms) at a relatively low-cost  (< 1000USD). We tested Oculomatic during regular monkey training and task performance in two independent laboratories and compared Oculomatic performance to existing scleral search-coils. While being fully non-invasive, Oculomatic performed favorably to the gold standard of search-coils with only a slight decrease in spatial accuracy.

We propose this system can support a range of research into the properties and neural mechanisms of oculomotor behavior as well as provide an affordable tool to scale non-human primate electrophysiology further.


The most recent version of the software can be found at:

Zimmermann, J., Vazquez, Y., Glimcher, P. W., Pesaran, B., & Louie, K. (2016). Oculomatic: High speed, reliable, and accurate open-source eye tracking for humans and non-human primates. Journal of Neuroscience Methods, 270, 138-146.

Laubach Lab GitHub Repository

The Laubach Lab at American University investigates executive control and decision making, focusing on the role of the prefrontal cortex. Through their GitHub repository, these researchers provide 3D print files for many of the behavioral devices used in their lab, including a Nosepoke and a Lickometer designed from rats. The repository also includes a script that reads MedPC files into Python in a usable way.

Wave Surfer

WaveSurfer is an open-source application for neurophysiology data acquisition and analysis. The program is based in MatLab, and evolved from an earlier open-source software package called Ephus. WaveSurfer is currently pre-release, but can be downloaded from the WaveSurfer Webpage or the WaveSurfer GitHub Repository.

The project was initiated by the Svoboda Lab, and developed as a collaborative effort between several research groups at the Howard Hughes Medical Institute’s Janelia Research Campus. Janelia is a major proponent of collaboration and open-science, providing documentation for dozens of tools and innovations developed on their campus through their webpage, including several tools specific to behavioral neuroscience research.