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Welcome to NeuroCarto's documentation!
=======================================

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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
--------

- [x] Read/Visualize/Modify/Write Neuropixels channelmap files (``*.imro``).

  - [x] Read Neuropixels channelmap files from other supported file format in GUI.
  - [x] (Experimental) set bad electrodes

- [x] Read SpikeGLX meta file (``*.meta``).

  - [x] Read Neuropixels probe serial number

- [x] Read/Visualize/Modify/Write Blueprint (a blueprint for generating a channelmap by a programming way).

  - [x] show conflict areas.

- [x] Show Atlas mouse brain as a background image.

  - [x] utilities functions for controlling the atlas image.
  - [x] probe coordinate functions

- [x] Customize electrode selection and probe kind.
- [x] Show channel efficiency and electrode density.
- [x] (Experimental) Show an image file as a background image (``--view=file``, ``--view=IMAGE``).

  - [ ] Read image resolution tags.

- [x] Show dynamic generated image (via ``matplotlib``) as a background image.
- [x] Run custom scripts (``--view=script``).

  - [x] give an example script to initial a blueprint based on an experimental data.
  - [ ] (Experimental) provided scripts

- [x] (Experimental) Record/Save/Load/Replay channelmap manipulate steps (``--view=history``)



Contents
--------

.. toctree::
    :maxdepth: 2

    install
    start
    views
    tutorial


Support formats
---------------

==================== ============================
package\\probe       Neuropixels family
==================== ============================
SpikeGLX ``*.imro``  read/write
SpikeGLX ``*.meta``  read
probeinterface [1]_  read/write
pandas [1]_          write [2]_
polars [1]_          write [2]_
==================== ============================

.. [1] optional dependency package
.. [2] convert channelmap as dataframe.

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
-------------

.. toctree::
    :maxdepth: 1

    api/neurocarto.rst

Contact Us
----------


.. toctree::
    :maxdepth: 1

    contact


Indices and tables
------------------

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`