NeuroCarto: A Neuropixels Channelmap Editor

PyPI - Python Version

NeuroCarto is a neural probe channel map editor for the Neuropixels probe family. It allows user to create a blueprint for arranging electrodes in a desired density and generate a custom channel map.

Electrode_Selection

Features

Read/Visualize/Modify/Write Neuropixels channelmap files (*.imro).
Read SpikeGLX meta file (*.meta).
Read/Visualize/Modify/Write Blueprint (a blueprint for generating a channelmap by a programming way).
Show Atlas mouse brain as a background image.
Customize electrode selection and probe kind.
Show channel efficiency and electrode density.

Blueprint

Relevant Papers

Su, TS., Kloosterman, F. NeuroCarto: A Toolkit for Building Custom Read-out Channel Maps for High Electrode-count Neural Probes. Neuroinform 23, 1–16 (2025). https://doi.org/10.1007/s12021-024-09705-2

Documentation

Please check Documentation for more details.

Install and Run

prepare environment.

Require Python 3.11.

Install

pip install neurocarto

Run

neurocarto

Optional dependency

brainglobe-atlasapi Atlas Brain background image supporting.
Pillow, tifffile other background image format supporting.
probeinterface probe/channelmap format import/export
pandas, polars channelmap data export.

Full optional dependencies are list in requirements-opt.txt.

Build from source

Please check the install page in the wiki.

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Source Distribution

neurocarto-0.2.2.tar.gz (176.1 kB view details)

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