/!\ Should not be used anymore as the developement moved into the https://github.com/SpikeInterface/probeinterface.

py-channelmap

Python tools to create channelmaps:

• for different probes :
  • Neuropixels (from spikeGLX and later from OpenEphys)
  • Tetrodes
  • More to come ...

The focus is set on an uniform way to create a channelmap without worrying of the implementation behind. Because of the probe class and the probe template, the way to create and display a channelmap is always identical with the exception of indicating the type of probes used and their options.

Installation

User mode

  pip install git+https://github.com/nerf-common/channelmap-generation.git

Developper mode

  git clone https://github.com/nerf-common/channelmap-generation.git
  cd channelmap-generation
  python setup.py build_ext --inplace
  pip install -e .

Usage

Neuropixels probes from spikeGLX

from py_channelmap import probes

hdw = probes("neuropixels", "*.ap.meta")

Tetrodes

1 mandatory argument :

• number of tetrodes used

1 optional argument:

• spacing : space between column (default : 200)

  hdw =  probes("tetrodes", nb_tetrode, spacing = spacing)

Read from a already existing channelmap You can also read and transform in another format an already existing channelmap file.

  hdw =  probes.read_from("path/to/*.channelmap")

Create and draw your channelmap

2 optional arguments:

• path = saving path of the channelmap. Sometime this parameter is already set in the implementation (neuropixels), sometime not (tetrodes), Using this option will override others paths previously generated.
• map_format : format to save
  • channelmap (default) : csv format with headers
  • mat : matlab format
  • prb : prb format

It will generate the adequat channelmap file + a txt file linking the hardware electrod id with the acquisition number (often called channel id in the channelmap)

  hdw.create_channel_map(path=path, map_format="channelmap")
  hdw.draw()