Tools for generating stimuli, stimulating and acquiring analog and digital signals using DAQ boards. Has tools for patch clamping electrophysiology and in the future to control galvo photostimulation. https://github.com/jcouto/labdaq
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Binary file viewer and memory mapping inteface for spikeGLX files. Example notebooks for unpacking sync channels and parse sorting results. This is part of the workshop material for the neuropixels workshop for the ParisNeuro Course 2019. https://github.com/jcouto/pnc_spks
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Tools to manually register widefield data and two-photon planes to the Allen Common Coordinate Framework. https://bitbucket.org/jpcouto/wfield/
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Arduino based controller to interface with experimental hardware for experiment control and logging. Allows controlling multiple setups with the same computer and recording pulses from cameras or other devices. Includes software for training on a linear treadmill and an interface written in bokeh. https://bitbucket.org/jpcouto/lineartreadmillrig
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Visual stimulation and experiment control with an arduino. Can interface with labcams, scanbox and spikeGLX to set names and initiate experiments accross computers. Configuration through a json configuration file, parameter definition for visual stimuli using text files. Actuators can be connected to airpuff valves or eye shutters and synchronized to the visual stimuli. Interfaces with https://bitbucket.org/jpcouto/lineartreadmillrig for signal acquisition and hardware control. https://bitbucket.org/jpcouto/pyvstim
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Camera interface and graphical user interface written in python, can record from multiple cameras and do real-time eye tracking. Can also perform histogram equalization and background subtraction. At the moment supports AVT, QImaging, PCO and generic cameras through the openCV interface. Uses https://bitbucket.org/jpcouto/mptracker for tracking the eye. https://bitbucket.org/jpcouto/labcams
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Pupil tracking written in python openCV bindings that can handle 5 min data(at 30Hz) in 10 seconds on a laptop using multiprocessing. Can be used in for real-time tracking in conjunction with labcams. https://bitbucket.org/jpcouto/mptracker
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Software for hybrid closed loop electrophysiology experiments and real-time conductance simulation. Builds on a real-time linux kernel and a command line interface for reproducibility and automation of experimental workflows. In colaboration with Daniele Linaro. http://danielelinaro.github.io/dynclamp/
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NEURON models and scripts for in silico experiments. Includes examples of extracellular and phase response curve simulations. Includes the McIntyre and Grill 2002, Traub et al. 2003, Khaliq and Raman 2002 and the De Schutter and Bower 1994 models. https://github.com/jcouto/neuron
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