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‎LICENSE‎

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Copyright (c) 2026 Toomas Erik Anijärv
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
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IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
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DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
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OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE
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OR OTHER DEALINGS IN THE SOFTWARE.

‎README.md‎

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![logo](docs/assets/yabplot_logo.png)
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**yabplot** is a Python library for creating beautiful, publication-quality 3D brain visualizations. it supports plotting cortical regions, subcortical structures, and white matter bundles, built on top of [PyVista](https://docs.pyvista.org/).
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[![PyPI version](https://img.shields.io/pypi/v/yabplot.svg)](https://pypi.org/project/yabplot/)
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[![Docs](https://github.com/teanijarv/yabplot/actions/workflows/docs.yml/badge.svg)](https://teanijarv.github.io/yabplot/)
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[![Tests](https://github.com/teanijarv/yabplot/actions/workflows/tests.yml/badge.svg)](https://github.com/teanijarv/yabplot/actions/workflows/tests.yml)
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<!-- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.XXXXXX.svg)](https://doi.org/10.5281/zenodo.XXXXXX) -->
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**yabplot** is a Python library for creating beautiful, publication-quality 3D brain visualizations. it supports plotting cortical regions, subcortical structures, and white matter bundles.
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the idea is simple. while there are already amazing visualization tools available, they often focus on specific domains—using one tool for white matter tracts and another for cortical surfaces inevitably leads to inconsistent styles. i wanted a unified, simple-to-use tool that enables me (and hopefully others) to perform most brain visualizations in a single place. recognizing that neuroscience evolves daily, i designed **yabplot** to be modular: it supports standard pre-packaged atlases out of the box, but easily accepts any custom parcellation or tractography dataset you might need.
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## quick start
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please refer to the documentation and examples for comprehensive guides.
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please refer to the [documentation](https://teanijarv.github.io/yabplot/) for more comprehensive guides.
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```python
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import yabplot as yab
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import numpy as np
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# plot random data on cortical regions
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regions = yab.get_atlas_regions('schaefer_400', 'cortical')
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data = np.random.rand(len(regions))
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yab.plot_cortical(data=data, atlas='schaefer_400', cmap='viridis')
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# see available cortical atlases
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atlases = yab.get_available_resources(category='cortical')
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# plot values for specific subcortical regions
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data = {'Left_Amygdala': 0.8, 'Right_Thalamus': 0.5}
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yab.plot_subcortical(data=data, atlas='aseg', views=['left_lateral', 'superior'])
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# see the region names within the aseg atlas
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regions = yab.get_atlas_regions(atlas='aseg', category='subcortical')
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# plot data on cortical regions
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data = np.arange(0, 1, 0.001)
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yab.plot_cortical(data=data, atlas='schaefer_1000', figsize=(600, 300),
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cmap='viridis', vminmax=[0, 1], style='default',
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views=['left_lateral', 'superior', 'right_lateral'])
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# plot values for specific white matter bundles
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data = {'FMaj': 0.2, 'FMin': -0.3}
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yab.plot_tracts(data=data, atlas='xtract_tiny', style='matte')
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# plot values for specific subcortical regions
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data = {'Left_Amygdala': 0.8, 'Right_Hippocampus': 0.5,
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'Right_Thalamus': -0.5, 'Left_Putamen': -1}
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yab.plot_subcortical(data=data, atlas='aseg', figsize=(600, 450), layout=(2, 2),
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views=['superior', 'anterior', 'left_lateral', 'right_lateral'],
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cmap='coolwarm', vminmax=[-1, 1], style='matte')
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# plot data on white matter bundles
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regions = yab.get_atlas_regions(atlas='xtract_tiny', category='tracts')
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data = np.arange(0, len(regions))
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yab.plot_tracts(data=data, atlas='xtract_tiny', figsize=(600, 300),
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views=['superior', 'anterior', 'left_lateral'], nan_color='#cccccc',
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bmesh_type='fsaverage', style='default', cmap='plasma')
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```
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![examples](docs/assets/examples.png)
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## acknowledgements
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yabplot relies on the extensive work of the neuroimaging community. if you use these atlases in your work, please cite the original authors.

‎docs/assets/examples.png‎

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‎docs/index.md‎

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![logo](assets/yabplot_logo.png)
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**yabplot** is a Python library for creating beautiful, publication-quality 3D brain visualizations. it supports plotting cortical regions, subcortical structures, and white matter bundles, built on top of [PyVista](https://docs.pyvista.org/).
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[![PyPI version](https://img.shields.io/pypi/v/yabplot.svg)](https://pypi.org/project/yabplot/)
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[![Docs](https://github.com/teanijarv/yabplot/actions/workflows/docs.yml/badge.svg)](https://teanijarv.github.io/yabplot/)
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[![Tests](https://github.com/teanijarv/yabplot/actions/workflows/tests.yml/badge.svg)](https://github.com/teanijarv/yabplot/actions/workflows/tests.yml)
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<!-- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.XXXXXX.svg)](https://doi.org/10.5281/zenodo.XXXXXX) -->
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**yabplot** is a Python library for creating beautiful, publication-quality 3D brain visualizations. it supports plotting cortical regions, subcortical structures, and white matter bundles.
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the idea is simple. while there are already amazing visualization tools available, they often focus on specific domains—using one tool for white matter tracts and another for cortical surfaces inevitably leads to inconsistent styles. i wanted a unified, simple-to-use tool that enables me (and hopefully others) to perform most brain visualizations in a single place. recognizing that neuroscience evolves daily, i designed **yabplot** to be modular: it supports standard pre-packaged atlases out of the box, but easily accepts any custom parcellation or tractography dataset you might need.
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## quick start
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please refer to the documentation and examples for comprehensive guides.
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please refer to the [documentation](https://teanijarv.github.io/yabplot/) for more comprehensive guides.
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```python
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import yabplot as yab
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import numpy as np
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# plot random data on cortical regions
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regions = yab.get_atlas_regions('schaefer_400', 'cortical')
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data = np.random.rand(len(regions))
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yab.plot_cortical(data=data, atlas='schaefer_400', cmap='viridis')
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# see available cortical atlases
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atlases = yab.get_available_resources(category='cortical')
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# plot values for specific subcortical regions
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data = {'Left_Amygdala': 0.8, 'Right_Thalamus': 0.5}
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yab.plot_subcortical(data=data, atlas='aseg', views=['left_lateral', 'superior'])
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# see the region names within the aseg atlas
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regions = yab.get_atlas_regions(atlas='aseg', category='subcortical')
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# plot data on cortical regions
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data = np.arange(0, 1, 0.001)
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yab.plot_cortical(data=data, atlas='schaefer_1000', figsize=(600, 300),
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cmap='viridis', vminmax=[0, 1], style='default',
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views=['left_lateral', 'superior', 'right_lateral'])
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# plot values for specific white matter bundles
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data = {'FMaj': 0.2, 'FMin': -0.3}
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yab.plot_tracts(data=data, atlas='xtract_tiny', style='matte')
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# plot values for specific subcortical regions
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data = {'Left_Amygdala': 0.8, 'Right_Hippocampus': 0.5,
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'Right_Thalamus': -0.5, 'Left_Putamen': -1}
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yab.plot_subcortical(data=data, atlas='aseg', figsize=(600, 450), layout=(2, 2),
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views=['superior', 'anterior', 'left_lateral', 'right_lateral'],
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cmap='coolwarm', vminmax=[-1, 1], style='matte')
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# plot data on white matter bundles
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regions = yab.get_atlas_regions(atlas='xtract_tiny', category='tracts')
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data = np.arange(0, len(regions))
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yab.plot_tracts(data=data, atlas='xtract_tiny', figsize=(600, 300),
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views=['superior', 'anterior', 'left_lateral'], nan_color='#cccccc',
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bmesh_type='fsaverage', style='default', cmap='plasma')
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```
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![examples](assets/examples.png)
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## acknowledgements
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yabplot relies on the extensive work of the neuroimaging community. if you use these atlases in your work, please cite the original authors.

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