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| | __ | |_ | | __ _ __ _ | |/ | '_ \ / _ |/ |/ _ | | | (| | |) | (| | (| | (| | ||_,|_./ _,|_,|_, | | | || https://github.com/jcouto/labdaq

Tools to control daq hardware for ephys or stimulation. This is currently under development.

Supported features:

• interfacing with an AXON 700B amplifier using telegraph input
• stimuli generation
• GUI for patch clamping (seal test, synchrounous acquisition)
• support for NI devices (tested with the PCI 6229)

Usage:

The first time it is ran it creates a configuration file in $HOME/labdaq/default/prefs.json

This configuration file specifies 3 things:

• channel_modes the available modes for all channels.
• channels list of channels.
• recorder options which specifies the format and the datapath

channel_modes

These can have different units and conversion factors. Each mode can have different settings for input and output.

Example:

    "channel_modes": {
        "analog": {
            "description": "regular_output",
            "input_conversion": 1,
            "input_units": "V",
            "output_conversion": 1,
            "output_units": "V"
        },
        "cc": {
            "description": "current clamp",
            "input_conversion": 100,
            "input_units": "pA",
            "output_conversion": 5e-05,
            "output_units": "mV"
        },
        "ttl": {
            "description": "TTL digital logic",
            "input_conversion": 1,
            "input_units": "na",
            "output_conversion": 1,
            "output_units": "na"
        },
        "vc": {
            "description": "voltage clamp",
            "input_conversion": 1000,
            "input_units": "pA",
            "output_conversion": 0.05,
            "output_units": "mV"
        }
    }

channels

Each channel must specify:

• the name
• the device to use (use the driver:device notation)
• the type of channel (e.g. analog_output)
• the sampling rate acq_rate (in samples per sec)
• a list of valid channel modes and
• the acquisition range (in Volt)

Example:

This is for patch clamping with the axon 700B.

    "channels": [
        {
            "acq_rate": 40000,
            "channel": "ai0",
            "device": "ni:Dev2",
            "modes": [
                "vc",
                "cc"
            ],
            "name": "ephys_in",
            "range": [
                -10,
                10
            ],
            "type": "analog_input"
        },
        {
            "acq_rate": 40000,
            "channel": "ao0",
            "device": "ni:Dev2",
            "modes": [
                "vc",
                "cc"
            ],
            "name": "ephys_out",
            "range": [
                -10,
                10
            ],
            "type": "analog_output"
        },
        {
            "acq_rate": 40000,
            "channel": "port0",
            "device": "ni:Dev2",
            "modes": [
                "ttl"
            ],
            "name": "opto_out",
            "type": "digital_port"
        },
        {
            "acq_rate": 40000,
            "channel": "ao2",
            "device": "ni:Dev2",
            "modes": [
                "analog"
            ],
            "name": "analogstim_out",
            "range": [
                -5,
                5
            ],
            "type": "analog_output"
        },
        {
            "channel": "ai1",
            "device": "ni:Dev2",
            "modes": [
                "analog"
            ],
            "name": "ephys_mode",
            "type": "axon200B_mode"
        }
    ],

Using the command line

Launch with labdaq. More options will be described here.

Installation

Clone the repository. Install from the code folder using python setup.py develop

Dependencies:

• numpy
• scipy
• matplotlib
• pyqt5
• pyqtgraph
• pandas
• hdf5
• nidaqmx (for using NI cards)

More on the installation will come here.