Metadata-Version: 2.4
Name: neurocarto
Version: 0.2.0
Summary: A web-interface channelmap editor for Neuropixels probe familiy
Author-email: Ta-Shun Su <antoniost29@gmail.com>
License: BSD 3-Clause License
        
        Copyright (c) 2023, AntonioST
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        1. Redistributions of source code must retain the above copyright notice, this
           list of conditions and the following disclaimer.
        
        2. Redistributions in binary form must reproduce the above copyright notice,
           this list of conditions and the following disclaimer in the documentation
           and/or other materials provided with the distribution.
        
        3. Neither the name of the copyright holder nor the names of its
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        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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Project-URL: Homepage, https://github.com/AntonioST/NeuroCarto
Project-URL: Documentation, https://neurocarto.readthedocs.io/en/latest/
Project-URL: Repository, https://github.com/AntonioST/NeuroCarto
Project-URL: Issues, https://github.com/AntonioST/NeuroCarto/issues
Keywords: Electrophysiology,Neuropixels,Channelmap
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Environment :: Web Environment
Classifier: Environment :: Console
Classifier: Topic :: Scientific/Engineering
Classifier: Intended Audience :: Science/Research
Classifier: Typing :: Typed
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: matplotlib
Requires-Dist: typing_extensions
Requires-Dist: bokeh
Provides-Extra: full
Requires-Dist: probeinterface; extra == "full"
Requires-Dist: brainglobe-atlasapi; extra == "full"
Requires-Dist: Pillow; extra == "full"
Requires-Dist: tifffile; extra == "full"
Requires-Dist: pandas; extra == "full"
Requires-Dist: polars; extra == "full"
Provides-Extra: doc
Requires-Dist: sphinx; extra == "doc"
Requires-Dist: jupyter; extra == "doc"
Requires-Dist: jupyter_contrib_nbextensions; extra == "doc"
Requires-Dist: nbsphinx; extra == "doc"
Requires-Dist: sphinx-rtd-theme; extra == "doc"
Requires-Dist: sphinx-markdown-builder; extra == "doc"
Dynamic: license-file

NeuroCarto: A Neuropixels Channelmap Editor
===========================================

[![PyPI - Version](https://img.shields.io/pypi/v/neurocarto)](https://pypi.org/project/neurocarto/)
![PyPI - Python Version](https://img.shields.io/pypi/pyversions/neurocarto)
[![Documentation Status](https://readthedocs.org/projects/neurocarto/badge/?version=latest)](https://neurocarto.readthedocs.io/en/latest/?badge=latest)

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](doc/source/_static/ani-electrode-selection.gif)

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](doc/source/_static/ani-blueprint.gif)

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](https://neurocarto.readthedocs.io/en/latest/) for more details.

Install and Run
---------------

### prepare environment.

Require `Python 3.10`.

### Install

```shell
pip install neurocarto
```

### Run

```shell
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](requirements-opt.txt).

Build from source
-----------------

Please check [install](https://github.com/AntonioST/chmap_editor/wiki/install) page in wiki.


