NeuroCarto: A Neuropixels Channelmap Editor

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.

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.

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

Documents

Please check Documentation for more details.

Install and Run

prepare environment.

Require Python 3.10.

Install

pip install neurocarto

Run

neurocarto

Optional dependency

• bg-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 install page in wiki.