Tools

Tools developed in-house.

pype: python physiology environment

Linux/Python-based realtime data collection system for visual psychophysics and neurophysiology is available at github, along with instructions for installation and basic setup.

The 100% open source system provides a framework for task-control, complex visual stimulus generation using Numpy, synchronously interfaces with both Plexon and TDT neurophysiological recording systems (or a simple schmidt trigger), video eye tracking systems from SR-Research, ISCAN and/or search coils. The system is readily capable of 60Hz full-screen video (or better) using off-the-shelf NVIDIA cards while synchronously recording spike and behavioral data at 1 kHz on standard (Ubunut/Mint) PC.

Tools are available to import data streams into MATLAB or do your analysis in python using Numpy (or any other python package).

elog – electronic lab notebook

elog is a pype-aware electronic lab notebook and automatic data logging system. Lab notebook data is stored in MySQL database and accesses via a simple, platform independent GUI program. ELog provides a simple python API that is used by pype to inject information about datafile names etc into the notebook automatically. Python, shell and MATLAB tools are provided for querying the elog database and facilitating automatic batched data analysis.

tdt2hdf5COMING SOON

Package to convert TDT Datatanks into HDF5 datafiles that can be easily and efficiently read in MATLAB, Python etc.

unispikeCOMING SOON

Unified matlab toolbox for reading and manipulating spike and LFP data recorded using the Plexon and TDT backends for pype. Unispike provides a standardized trial-based view of the physiological data streams recorded by the data acquisition hardware synchronized (within 1ms) to the behavioral/stimulus datastream recorded by pype.

Other peoples’ tools that we depend on.

Linux
We use mostly Mint and Ubuntu in the lab. Mint for desktops and Ubuntu for data collection.
Neurodebian
Handy repository for linux-based neuroscience tools. Precompiled packages for almost all the neuroscience-related tools we use that aren’t built in to Mint or Ubuntu.
NumPy
Numerical analysis tools for python (aka open-source Matlab alternative).
Pygame
Python OpenGL-based graphics.