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Welcome to NeuroCarto’s documentation!

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 Neuropixels channelmap files from other supported file format in GUI.
  • (Experimental) set bad electrodes
• Read SpikeGLX meta file (*.meta).
  • Read Neuropixels probe serial number
• Read/Visualize/Modify/Write Blueprint (a blueprint for generating a channelmap by a programming way).
  • show conflict areas.
• Show Atlas mouse brain as a background image.
  • utilities functions for controlling the atlas image.
  • probe coordinate functions
• Customize electrode selection and probe kind.
• Show channel efficiency and electrode density.
• (Experimental) Show an image file as a background image (--view=file, --view=IMAGE).
  • Read image resolution tags.
• Show dynamic generated image (via matplotlib) as a background image.
• Run custom scripts (--view=script).
  • give an example script to initial a blueprint based on an experimental data.
  • (Experimental) provided scripts
• (Experimental) Record/Save/Load/Replay channelmap manipulate steps (--view=history)

Contents

• Installation
  • Require
  • Install
  • Run
  • Optional dependency packages
  • Build from source
  • Build Document
  • testing library versions
• Get Start
  • Commandline options
  • Application View
  • Build your first channelmap
• View Components
  • User configuration
  • Builtin Components
  • Customize Components
• Tutorials
  • Example of using library code
  • Extending Guideline
  • Electrode selecting
  • Extending view component
  • Statistics

Support formats

package\probe	Neuropixels family
SpikeGLX *.imro	read/write
SpikeGLX *.meta	read
probeinterface	read/write
pandas	write
polars	write

Support probe kinds

Neuropixels probe family

file format: *.imro.

probe (code)\state	read	write
Neuropixels 1.0 (0/1000)	yes	yes
Neuropixels 2.0 (21/2000)	yes	yes
Neuropixels 2.0 (2003)	yes	yes
4-shank Neuropixels 2.0 (24/2010)	yes	yes
4-shank Neuropixels 2.0 (24/2013)	yes	yes
NHP	no	no
UHD	no	no
Opto	no	no
NXT	no	no

API Reference

Please check API for more details.