subcortex-visualization 1.0.0__tar.gz → 1.2.0__tar.gz

{subcortex_visualization-1.0.0/subcortex_visualization.egg-info → subcortex_visualization-1.2.0}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: subcortex_visualization
-Version: 1.0.0
-Summary: A package to visualize subcortical brain data in two dimensions.
+Version: 1.2.0
+Summary: A package to visualize subcortical and cerebellar brain data in two dimensions.
 Author: Annie G. Bryant
 Author-email: "Annie G. Bryant" <anniegbryant@gmail.com>
 License: GNU General Public License v3 (GPLv3)
@@ -27,30 +27,29 @@ Dynamic: license-file
 
 [![DOI](https://zenodo.org/badge/965897997.svg)](https://doi.org/10.5281/zenodo.15385315)
 
-This python package currently includes the following six subcortical atlases for data visualization in two-dimensional vector graphics:
+This package (implemented in Python and R) currently includes the following nine subcortical and cerebellar atlases for data visualization in two-dimensional vector graphics:
 
 <img src="docs-site/docs/images/all_atlas_showcase.png" width="100%">
 
 More information about these atlases, including the process of rendering the surfaces and tracing the outlines for each, can be found in the [`atlas_info/`](https://github.com/anniegbryant/subcortex_visualization/tree/main/atlas_info) directory and at the [project website](https://anniegbryant.github.io/subcortex_visualization/).
 
-
 ## 🙋‍♀️ Motivation
 
-This Python package was created to generate two-dimensional subcortex images in the style of the popular [`ggseg` package](https://github.com/ggseg/ggseg) in R.
-We based our vector graphic outlines on the three-dimensional subcortical meshes either (1) provided as part of the [ENIGMA toolbox](https://github.com/MICA-MNI/ENIGMA) for the aseg atlas or (2) meshes generated in-house using rendering software from [Chris Rorden's lab](https://github.com/neurolabusc) (either [nii2mesh](https://github.com/neurolabusc/nii2mesh) or [Surf Ice](https://github.com/neurolabusc/surf-ice); check out [`custom_segmentation_pipeline/`](https://github.com/anniegbryant/subcortex_visualization/tree/main/custom_segmentation_pipeline) for more information).
-
-The below graphic summarizes the transformation from 3D volumetric meshes to 2D surfaces, starting from the ENIGMA toolbox ('aseg' atlas, left) or a custom-rendered mesh from the [Melbourne Subcortex Atlas](https://github.com/yetianmed/subcortex/tree/master) as published in [Tian et al. (2020)]()https://www.nature.com/articles/s41593-020-00711-6 -- ('S1' granularity level, right).
-
-<img src="docs-site/docs/images/aseg_and_Melbourne_S1_3D_to_2D_schematic.png" width="90%">
+This visualization package was created to generate two-dimensional subcortex images in the style of the popular [`ggseg` package](https://github.com/ggseg/ggseg) in R.
+We based our vector graphic outlines on the three-dimensional subcortical meshes either (1) provided as part of the [ENIGMA toolbox](https://github.com/MICA-MNI/ENIGMA) for the aseg atlas or (2) meshes generated in-house using rendering software from [Chris Rorden's lab](https://github.com/neurolabusc) ([Surf Ice](https://github.com/neurolabusc/surf-ice); check out [`custom_segmentation_pipeline/`](https://github.com/anniegbryant/subcortex_visualization/tree/main/custom_segmentation_pipeline) for more information).
 
+The below graphic summarizes the transformation from 3D volumetric meshes to 2D surfaces, starting from the [Melbourne Subcortex Atlas](https://github.com/yetianmed/subcortex/tree/master) as published in [Tian et al. (2020)](https://www.nature.com/articles/s41593-020-00711-6) at the 'S1' resolution.
 
-While `ggseg` offers subcortical plotting with the `aseg` atlas, it is [not currently possible](https://github.com/ggseg/ggseg/issues/104) to show data from all seven subcortical regions (accumbens, amygdala, caudate, hippocampus, pallidum, putamen, thalamus) in the same figure.
-Moreover, there is currently no other software available to visualize any of the other above subcortical/thalamic atlases in 2D with real data, hence development here.
+<img src="docs-site/docs/images/Melbourne_S1_subcortical_atlas_info.png" width="90%">
 
+While [`ggseg`](https://github.com/ggseg/ggseg) offers subcortical plotting with the `aseg` atlas, it is [not currently possible](https://github.com/ggseg/ggseg/issues/104) to show data from all seven subcortical regions (accumbens, amygdala, caudate, hippocampus, pallidum, putamen, thalamus) in the same figure.
+Moreover, there is currently no other software available to visualize any of the other above subcortical, thalamic, or cerebellar atlases in two dimensions with real data, motivating the development of this package.
 
 ## 🖥️ Installation
 
-The package can be installed from GitHub in two ways.
+### Python 
+
+The Python version of this package can be installed in two ways.
 First, you can install directly with pip from the [PyPI repository](https://pypi.org/project/subcortex-visualization/):
 
 ```bash
@@ -67,11 +66,23 @@ pip install .
 
 This will install the `subcortex_visualization` package so you have access to the `plot_subcortical_data` function and associated data.
 
+### R
+
+The R version of this package can be installed from GitHub within R using the `remotes` package as follows:
+
+```R
+# if not already installed
+install.packages("remotes")
+
+# then install subcortexVisualizationR
+remotes::install_github("anniegbryant/subcortex_visualization", subdir = "subcortexVisualizationR"
+```
+
 ## 👨‍💻 Usage
 
 ### ❗️ Quick start
 
-Running the below code will produce an image of the left subcortex in the aseg atlas (the default), each region colored by its index, with the plasma color scheme:
+Running the code below (in either python or R) will produce an image of the left subcortex in the aseg atlas (the default), each region colored by its index, with the plasma color scheme:
 
 ```python
 plot_subcortical_data(hemisphere='L', cmap='plasma', 
@@ -84,7 +95,7 @@ plot_subcortical_data(hemisphere='L', cmap='plasma',
 ### 📚 Tutorial
 
 For a guide that goes through all the functionality and atlases available in this package, we compiled a simple walkthrough tutorial in [tutorial.ipynb](https://github.com/anniegbryant/subcortex_visualization/blob/main/tutorial.ipynb).
-To plot real data in the subcortex, your `subcortex_data` should be  a `pandas.DataFrame` structured as follows (here we've just assigned an integer index to each region):
+To plot real data in the subcortex, your `subcortex_data` should be a Python `pandas.DataFrame` or an R `data.frame` structured as follows (here we've just assigned an integer index to each region):
 
 | region        | value         | Hemisphere  |
 | :--- | :---: | :---: |
@@ -98,18 +109,18 @@ To plot real data in the subcortex, your `subcortex_data` should be  a `pandas.D
 
 Briefly, all functionality is contained within the `plot_subcortical_data` function, which takes in the following arguments: 
 * `subcortex_data`: The three-column dataframe in a format as shown above; this is optional, if left out the plot will just color each region by its index
-* `atlas`: The name of the subcortical segmentation atlas (default is 'aseg', all options listed below)
+* `atlas`: The name of the subcortical, thalamic, or cerebellar segmentation atlas (default is 'aseg', all options listed below)
 * `value_column`: The name of the column in your `subcortex_data` to plot, defaults to 'value'
-* `line_thickness`: How thick the lines around each subcortical region should be drawn, in mm (default is 1.5)
+* `line_thickness`: How thick the lines around each subcortical region should be drawn
 * `line_color`: What color the lines around each subcortical region should be (default is 'black')
 * `hemisphere`: Which hemisphere ('L' or 'R') the `subcortex_data` is from; can also be 'both' (default is 'L')
 * `fill_title`: Name to add to legend (default is 'values')
-* `cmap`: name of colormap (e.g., 'plasma' or 'viridis') or a `matplotlib.colors.Colormap` (default is 'viridis')
+* `cmap`: name of colormap (e.g., 'plasma' or 'viridis') or a `matplotlib.colors.Colormap` (default is 'viridis'); for R, this could be a vector of discrete colors or a color palette generating function
 * `vmin`: Min fill value; this is optional, and you would only want to use this to manually constrain the fill range to match another figure
 * `vmax`: Max fill value; this is optional, and you would only want to use this to manually constrain the fill range to match another figure
 * `midpoint`: Midpoint value to enforce for fill range; this is optional
 
-Here's an example plotting both hemispheres, with data randomly sampled from a normal distribution, setting a color range from blue (low) to red (high) with white at the center (midpoint=0):
+Here's an example in Python for plotting both hemispheres, with data randomly sampled from a normal distribution, setting a color range from blue (low) to red (high) with white at the center (midpoint=0):
 
 ```python
 import matplotlib.colors as mcolors
@@ -134,31 +145,38 @@ plot_subcortical_data(subcortex_data=example_continuous_data, atlas='aseg',
 
 ### Available atlases
 
-The following six subcortical atlases are currently supported with more information at the [project website](https://anniegbryant.github.io/subcortex_visualization/atlas_info/): 
+The following nine subcortical atlases are currently supported with more information at the [project website](https://anniegbryant.github.io/subcortex_visualization/atlas_info/): 
 
 * `aseg`: The `aseg` parcellation atlas from FreeSurfer
 * `Melbourne_S1`: The Melbourne Subcortex Atlas at granularity level S1, from [Tian et al. *Nature Neuroscience* (2020)](https://www.nature.com/articles/s41593-020-00711-6)
 * `Melbourne_S2`: The Melbourne Subcortex Atlas at granularity level S2, from [Tian et al. *Nature Neuroscience* (2020)](https://www.nature.com/articles/s41593-020-00711-6)
+* `Melbourne_S3`: The Melbourne Subcortex Atlas at granularity level S3, from [Tian et al. *Nature Neuroscience* (2020)](https://www.nature.com/articles/s41593-020-00711-6)
+* `Melbourne_S4`: The Melbourne Subcortex Atlas at granularity level S4, from [Tian et al. *Nature Neuroscience* (2020)](https://www.nature.com/articles/s41593-020-00711-6)
 * `AICHA`: The AICHA subcortex atlas, from [Joliot et al. *J Neurosci Methods* (2015)](https://pubmed.ncbi.nlm.nih.gov/26213217/).
 * `Brainnetome`: The Brainnetome subcortex atlas, from [Fan et al. *Cerebral Cortex* (2016)](https://pmc.ncbi.nlm.nih.gov/articles/PMC4961028/)
 * `Thalamus_Nuclei_HCP`: The thalamic nuclei atlas derived from HCP data, from [Najdenovska et al. *Scientific Data* (2018)](https://www.nature.com/articles/sdata2018270)
+* `SUIT`: The SUIT cerebellum atlas, from [Diedrichsen *Neuroimage* (2006)](https://doi.org/10.1016/j.neuroimage.2006.05.056)
 
 
 ## 💡 Want to generate your own mesh and/or parcellation?
 
 <img src="docs-site/docs/images/custom_vector_method.png" width="70%">
 
-This package provides six subcortical atlases as a starting point.
+This package provides nine subcortical, thalamic, and cerebellar atlases as a starting point.
 The workflow can readily be extended to your favorite segmentation atlas, though! 
 We have a dedicated folder for a custom segmentation pipeline that will walk you through the two key steps:  
-1. Rendering a series of triangulated surface meshes from your parcellation atlas (starting from a .nii.gz volume), using either the [`nii2mesh`](https://github.com/neurolabusc/nii2mesh) or [`surfice_atlas`](https://github.com/neurolabusc/surfice_atlas) software, both developed by [Chris Rorden's lab](https://github.com/rordenlab); and 
+1. Rendering a series of triangulated surface meshes from your parcellation atlas (starting from a .nii.gz volume), using the [`surfice_atlas`](https://github.com/neurolabusc/surfice_atlas) software, both developed by [Chris Rorden's lab](https://github.com/rordenlab); and 
 2. Tracing the outline of each region in the rendered mesh in vector graphic editing software (we use Inkscape in the tutorial as a powerful and free option), to yield a two-dimensional image of your atlas in scalable vector graphic (.svg) format.
 
 Check out the walkthrough in the [`custom_segmentation_pipeline/`](https://github.com/anniegbryant/subcortex_visualization/tree/main/custom_segmentation_pipeline) folder for more information on how to render your own volumetric segmentation with an interactive mesh and convert to a two-dimensional vector graphic that can be integrated with this package.
 
 ## 🙏 Acknowledgments
 
-Thank you very much to [Chris Rorden](https://github.com/rordenlab), [Ye Tian](https://github.com/yetianmed), and [Sid Chopra](https://github.com/sidchop) for their suggestions and continued development of open tools for neuroimaging visualization that enabled development of this project!
+Thank you very much to [Chris Rorden](https://github.com/rordenlab), [Ye Tian](https://github.com/yetianmed), and [Sid Chopra](https://github.com/sidchop) for their suggestions and continued development of open tools for neuroimaging visualization that enabled the development of this project!
+
+We're also very grateful for ongoing contributions from members of the GitHub community: 
+
+[![Contributors](https://contrib.rocks/image?repo=anniegbryant/subcortex_visualization)](https://github.com/anniegbryant/subcortex_visualization/graphs/contributors)
 
 ## 🔗 Citing this package
 

{subcortex_visualization-1.0.0 → subcortex_visualization-1.2.0}/README.md

@@ -2,30 +2,29 @@
 
 [![DOI](https://zenodo.org/badge/965897997.svg)](https://doi.org/10.5281/zenodo.15385315)
 
-This python package currently includes the following six subcortical atlases for data visualization in two-dimensional vector graphics:
+This package (implemented in Python and R) currently includes the following nine subcortical and cerebellar atlases for data visualization in two-dimensional vector graphics:
 
 <img src="docs-site/docs/images/all_atlas_showcase.png" width="100%">
 
 More information about these atlases, including the process of rendering the surfaces and tracing the outlines for each, can be found in the [`atlas_info/`](https://github.com/anniegbryant/subcortex_visualization/tree/main/atlas_info) directory and at the [project website](https://anniegbryant.github.io/subcortex_visualization/).
 
-
 ## 🙋‍♀️ Motivation
 
-This Python package was created to generate two-dimensional subcortex images in the style of the popular [`ggseg` package](https://github.com/ggseg/ggseg) in R.
-We based our vector graphic outlines on the three-dimensional subcortical meshes either (1) provided as part of the [ENIGMA toolbox](https://github.com/MICA-MNI/ENIGMA) for the aseg atlas or (2) meshes generated in-house using rendering software from [Chris Rorden's lab](https://github.com/neurolabusc) (either [nii2mesh](https://github.com/neurolabusc/nii2mesh) or [Surf Ice](https://github.com/neurolabusc/surf-ice); check out [`custom_segmentation_pipeline/`](https://github.com/anniegbryant/subcortex_visualization/tree/main/custom_segmentation_pipeline) for more information).
-
-The below graphic summarizes the transformation from 3D volumetric meshes to 2D surfaces, starting from the ENIGMA toolbox ('aseg' atlas, left) or a custom-rendered mesh from the [Melbourne Subcortex Atlas](https://github.com/yetianmed/subcortex/tree/master) as published in [Tian et al. (2020)]()https://www.nature.com/articles/s41593-020-00711-6 -- ('S1' granularity level, right).
-
-<img src="docs-site/docs/images/aseg_and_Melbourne_S1_3D_to_2D_schematic.png" width="90%">
+This visualization package was created to generate two-dimensional subcortex images in the style of the popular [`ggseg` package](https://github.com/ggseg/ggseg) in R.
+We based our vector graphic outlines on the three-dimensional subcortical meshes either (1) provided as part of the [ENIGMA toolbox](https://github.com/MICA-MNI/ENIGMA) for the aseg atlas or (2) meshes generated in-house using rendering software from [Chris Rorden's lab](https://github.com/neurolabusc) ([Surf Ice](https://github.com/neurolabusc/surf-ice); check out [`custom_segmentation_pipeline/`](https://github.com/anniegbryant/subcortex_visualization/tree/main/custom_segmentation_pipeline) for more information).
 
+The below graphic summarizes the transformation from 3D volumetric meshes to 2D surfaces, starting from the [Melbourne Subcortex Atlas](https://github.com/yetianmed/subcortex/tree/master) as published in [Tian et al. (2020)](https://www.nature.com/articles/s41593-020-00711-6) at the 'S1' resolution.
 
-While `ggseg` offers subcortical plotting with the `aseg` atlas, it is [not currently possible](https://github.com/ggseg/ggseg/issues/104) to show data from all seven subcortical regions (accumbens, amygdala, caudate, hippocampus, pallidum, putamen, thalamus) in the same figure.
-Moreover, there is currently no other software available to visualize any of the other above subcortical/thalamic atlases in 2D with real data, hence development here.
+<img src="docs-site/docs/images/Melbourne_S1_subcortical_atlas_info.png" width="90%">
 
+While [`ggseg`](https://github.com/ggseg/ggseg) offers subcortical plotting with the `aseg` atlas, it is [not currently possible](https://github.com/ggseg/ggseg/issues/104) to show data from all seven subcortical regions (accumbens, amygdala, caudate, hippocampus, pallidum, putamen, thalamus) in the same figure.
+Moreover, there is currently no other software available to visualize any of the other above subcortical, thalamic, or cerebellar atlases in two dimensions with real data, motivating the development of this package.
 
 ## 🖥️ Installation
 
-The package can be installed from GitHub in two ways.
+### Python 
+
+The Python version of this package can be installed in two ways.
 First, you can install directly with pip from the [PyPI repository](https://pypi.org/project/subcortex-visualization/):
 
 ```bash
@@ -42,11 +41,23 @@ pip install .
 
 This will install the `subcortex_visualization` package so you have access to the `plot_subcortical_data` function and associated data.
 
+### R
+
+The R version of this package can be installed from GitHub within R using the `remotes` package as follows:
+
+```R
+# if not already installed
+install.packages("remotes")
+
+# then install subcortexVisualizationR
+remotes::install_github("anniegbryant/subcortex_visualization", subdir = "subcortexVisualizationR"
+```
+
 ## 👨‍💻 Usage
 
 ### ❗️ Quick start
 
-Running the below code will produce an image of the left subcortex in the aseg atlas (the default), each region colored by its index, with the plasma color scheme:
+Running the code below (in either python or R) will produce an image of the left subcortex in the aseg atlas (the default), each region colored by its index, with the plasma color scheme:
 
 ```python
 plot_subcortical_data(hemisphere='L', cmap='plasma', 
@@ -59,7 +70,7 @@ plot_subcortical_data(hemisphere='L', cmap='plasma',
 ### 📚 Tutorial
 
 For a guide that goes through all the functionality and atlases available in this package, we compiled a simple walkthrough tutorial in [tutorial.ipynb](https://github.com/anniegbryant/subcortex_visualization/blob/main/tutorial.ipynb).
-To plot real data in the subcortex, your `subcortex_data` should be  a `pandas.DataFrame` structured as follows (here we've just assigned an integer index to each region):
+To plot real data in the subcortex, your `subcortex_data` should be a Python `pandas.DataFrame` or an R `data.frame` structured as follows (here we've just assigned an integer index to each region):
 
 | region        | value         | Hemisphere  |
 | :--- | :---: | :---: |
@@ -73,18 +84,18 @@ To plot real data in the subcortex, your `subcortex_data` should be  a `pandas.D
 
 Briefly, all functionality is contained within the `plot_subcortical_data` function, which takes in the following arguments: 
 * `subcortex_data`: The three-column dataframe in a format as shown above; this is optional, if left out the plot will just color each region by its index
-* `atlas`: The name of the subcortical segmentation atlas (default is 'aseg', all options listed below)
+* `atlas`: The name of the subcortical, thalamic, or cerebellar segmentation atlas (default is 'aseg', all options listed below)
 * `value_column`: The name of the column in your `subcortex_data` to plot, defaults to 'value'
-* `line_thickness`: How thick the lines around each subcortical region should be drawn, in mm (default is 1.5)
+* `line_thickness`: How thick the lines around each subcortical region should be drawn
 * `line_color`: What color the lines around each subcortical region should be (default is 'black')
 * `hemisphere`: Which hemisphere ('L' or 'R') the `subcortex_data` is from; can also be 'both' (default is 'L')
 * `fill_title`: Name to add to legend (default is 'values')
-* `cmap`: name of colormap (e.g., 'plasma' or 'viridis') or a `matplotlib.colors.Colormap` (default is 'viridis')
+* `cmap`: name of colormap (e.g., 'plasma' or 'viridis') or a `matplotlib.colors.Colormap` (default is 'viridis'); for R, this could be a vector of discrete colors or a color palette generating function
 * `vmin`: Min fill value; this is optional, and you would only want to use this to manually constrain the fill range to match another figure
 * `vmax`: Max fill value; this is optional, and you would only want to use this to manually constrain the fill range to match another figure
 * `midpoint`: Midpoint value to enforce for fill range; this is optional
 
-Here's an example plotting both hemispheres, with data randomly sampled from a normal distribution, setting a color range from blue (low) to red (high) with white at the center (midpoint=0):
+Here's an example in Python for plotting both hemispheres, with data randomly sampled from a normal distribution, setting a color range from blue (low) to red (high) with white at the center (midpoint=0):
 
 ```python
 import matplotlib.colors as mcolors
@@ -109,31 +120,38 @@ plot_subcortical_data(subcortex_data=example_continuous_data, atlas='aseg',
 
 ### Available atlases
 
-The following six subcortical atlases are currently supported with more information at the [project website](https://anniegbryant.github.io/subcortex_visualization/atlas_info/): 
+The following nine subcortical atlases are currently supported with more information at the [project website](https://anniegbryant.github.io/subcortex_visualization/atlas_info/): 
 
 * `aseg`: The `aseg` parcellation atlas from FreeSurfer
 * `Melbourne_S1`: The Melbourne Subcortex Atlas at granularity level S1, from [Tian et al. *Nature Neuroscience* (2020)](https://www.nature.com/articles/s41593-020-00711-6)
 * `Melbourne_S2`: The Melbourne Subcortex Atlas at granularity level S2, from [Tian et al. *Nature Neuroscience* (2020)](https://www.nature.com/articles/s41593-020-00711-6)
+* `Melbourne_S3`: The Melbourne Subcortex Atlas at granularity level S3, from [Tian et al. *Nature Neuroscience* (2020)](https://www.nature.com/articles/s41593-020-00711-6)
+* `Melbourne_S4`: The Melbourne Subcortex Atlas at granularity level S4, from [Tian et al. *Nature Neuroscience* (2020)](https://www.nature.com/articles/s41593-020-00711-6)
 * `AICHA`: The AICHA subcortex atlas, from [Joliot et al. *J Neurosci Methods* (2015)](https://pubmed.ncbi.nlm.nih.gov/26213217/).
 * `Brainnetome`: The Brainnetome subcortex atlas, from [Fan et al. *Cerebral Cortex* (2016)](https://pmc.ncbi.nlm.nih.gov/articles/PMC4961028/)
 * `Thalamus_Nuclei_HCP`: The thalamic nuclei atlas derived from HCP data, from [Najdenovska et al. *Scientific Data* (2018)](https://www.nature.com/articles/sdata2018270)
+* `SUIT`: The SUIT cerebellum atlas, from [Diedrichsen *Neuroimage* (2006)](https://doi.org/10.1016/j.neuroimage.2006.05.056)
 
 
 ## 💡 Want to generate your own mesh and/or parcellation?
 
 <img src="docs-site/docs/images/custom_vector_method.png" width="70%">
 
-This package provides six subcortical atlases as a starting point.
+This package provides nine subcortical, thalamic, and cerebellar atlases as a starting point.
 The workflow can readily be extended to your favorite segmentation atlas, though! 
 We have a dedicated folder for a custom segmentation pipeline that will walk you through the two key steps:  
-1. Rendering a series of triangulated surface meshes from your parcellation atlas (starting from a .nii.gz volume), using either the [`nii2mesh`](https://github.com/neurolabusc/nii2mesh) or [`surfice_atlas`](https://github.com/neurolabusc/surfice_atlas) software, both developed by [Chris Rorden's lab](https://github.com/rordenlab); and 
+1. Rendering a series of triangulated surface meshes from your parcellation atlas (starting from a .nii.gz volume), using the [`surfice_atlas`](https://github.com/neurolabusc/surfice_atlas) software, both developed by [Chris Rorden's lab](https://github.com/rordenlab); and 
 2. Tracing the outline of each region in the rendered mesh in vector graphic editing software (we use Inkscape in the tutorial as a powerful and free option), to yield a two-dimensional image of your atlas in scalable vector graphic (.svg) format.
 
 Check out the walkthrough in the [`custom_segmentation_pipeline/`](https://github.com/anniegbryant/subcortex_visualization/tree/main/custom_segmentation_pipeline) folder for more information on how to render your own volumetric segmentation with an interactive mesh and convert to a two-dimensional vector graphic that can be integrated with this package.
 
 ## 🙏 Acknowledgments
 
-Thank you very much to [Chris Rorden](https://github.com/rordenlab), [Ye Tian](https://github.com/yetianmed), and [Sid Chopra](https://github.com/sidchop) for their suggestions and continued development of open tools for neuroimaging visualization that enabled development of this project!
+Thank you very much to [Chris Rorden](https://github.com/rordenlab), [Ye Tian](https://github.com/yetianmed), and [Sid Chopra](https://github.com/sidchop) for their suggestions and continued development of open tools for neuroimaging visualization that enabled the development of this project!
+
+We're also very grateful for ongoing contributions from members of the GitHub community: 
+
+[![Contributors](https://contrib.rocks/image?repo=anniegbryant/subcortex_visualization)](https://github.com/anniegbryant/subcortex_visualization/graphs/contributors)
 
 ## 🔗 Citing this package
 

{subcortex_visualization-1.0.0 → subcortex_visualization-1.2.0}/pyproject.toml

@@ -4,11 +4,11 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "subcortex_visualization"
-version = "1.0.0"
+version = "1.2.0"
 authors = [
   { name="Annie G. Bryant", email="anniegbryant@gmail.com" },
 ]
-description = "A package to visualize subcortical brain data in two dimensions."
+description = "A package to visualize subcortical and cerebellar brain data in two dimensions."
 readme = "README.md"
 requires-python = ">=3.9"
 

{subcortex_visualization-1.0.0 → subcortex_visualization-1.2.0}/setup.py

@@ -10,13 +10,13 @@ install_requires = [
 
 setup(
     name='subcortex_visualization',
-    version='0.1.12',
+    version='1.2.0',
     description='Visualize subcortical brain data from SVG templates',
     author='Annie G. Bryant',
     packages=find_packages(),
     include_package_data=True,  # ← IMPORTANT
     package_data={
-        'subcortex_visualization': ['data/*.svg', 'data/*.csv'],
+        'subcortex_visualization': ['data/*.svg', 'data/*.csv', 'atlases/*.nii.gz', 'atlases/*.csv'],
     },
     install_requires=[
         'numpy',

subcortex_visualization-1.2.0/subcortex_visualization/atlases/AICHA_subcortex_lookup.csv

@@ -0,0 +1,40 @@
+345,Amygdala-1-lh
+346,Amygdala-1-rh
+347,Caudate-1-lh
+348,Caudate-1-rh
+349,Caudate-2-lh
+350,Caudate-2-rh
+351,Caudate-3-lh
+352,Caudate-3-rh
+353,Caudate-4-lh
+354,Caudate-4-rh
+355,Caudate-5-lh
+356,Caudate-5-rh
+357,Caudate-6-lh
+358,Caudate-6-rh
+359,Caudate-7-lh
+360,Caudate-7-rh
+361,Pallidum-1-lh
+362,Pallidum-1-rh
+363,Putamen-2-lh
+364,Putamen-2-rh
+365,Putamen-3-lh
+366,Putamen-3-rh
+367,Thalamus-1-lh
+368,Thalamus-1-rh
+369,Thalamus-2-lh
+370,Thalamus-2-rh
+371,Thalamus-3-lh
+372,Thalamus-3-rh
+373,Thalamus-4-lh
+374,Thalamus-4-rh
+375,Thalamus-5-lh
+376,Thalamus-5-rh
+377,Thalamus-6-lh
+378,Thalamus-6-rh
+379,Thalamus-7-lh
+380,Thalamus-7-rh
+381,Thalamus-8-lh
+382,Thalamus-8-rh
+383,Thalamus-9-lh
+384,Thalamus-9-rh

subcortex_visualization-1.2.0/subcortex_visualization/atlases/Brainnetome_subcortex_lookup.csv

@@ -0,0 +1,36 @@
+211,mAmyg-lh
+212,mAmyg-rh
+213,lAmyg-lh
+214,lAmyg-rh
+215,rHipp-lh
+216,rHipp-rh
+217,cHipp-lh
+218,cHipp-rh
+219,vCa-lh
+220,vCa-rh
+221,GP-lh
+222,GP-rh
+223,NAC-lh
+224,NAC-rh
+225,vmPu-lh
+226,vmPu-rh
+227,dCa-lh
+228,dCa-rh
+229,dlPu-lh
+230,dlPu-rh
+231,mPFtha-lh
+232,mPFtha-rh
+233,mPMtha-lh
+234,mPMtha-rh
+235,Stha-lh
+236,Stha-rh
+237,rTtha-lh
+238,rTtha-rh
+239,PPtha-lh
+240,PPtha-rh
+241,Otha-lh
+242,Otha-rh
+243,cTtha-lh
+244,cTtha-rh
+245,lPFtha-lh
+246,lPFtha-rh

subcortex_visualization-1.2.0/subcortex_visualization/atlases/Melbourne_S1_subcortex_lookup.csv

@@ -0,0 +1,16 @@
+1,hippocampus-rh
+2,amygdala-rh
+3,thalamus_posterior-rh
+4,thalamus_anterior-rh
+5,pallidum-rh
+6,accumbens-rh
+7,putamen-rh
+8,caudate-rh
+9,hippocampus-lh
+10,amygdala-lh
+11,thalamus_posterior-lh
+12,thalamus_anterior-lh
+13,pallidum-lh
+14,accumbens-lh
+15,putamen-lh
+16,caudate-lh

subcortex_visualization-1.2.0/subcortex_visualization/atlases/Melbourne_S2_subcortex_lookup.csv

@@ -0,0 +1,32 @@
+1,hippocampus_anterior-rh
+2,hippocampus_posterior-rh
+3,amygdala_lateral-rh
+4,amygdala_medial-rh
+5,thalamus_DP-rh
+6,thalamus_VP-rh
+7,thalamus_VA-rh
+8,thalamus_DA-rh
+9,accumbens_shell-rh
+10,accumbens_core-rh
+11,pallidum_posterior-rh
+12,pallidum_anterior-rh
+13,putamen_anterior-rh
+14,putamen_posterior-rh
+15,caudate_anterior-rh
+16,caudate_posterior-rh
+17,hippocampus_anterior-lh
+18,hippocampus_posterior-lh
+19,amygdala_lateral-lh
+20,amygdala_medial-lh
+21,thalamus_DP-lh
+22,thalamus_VP-lh
+23,thalamus_VA-lh
+24,thalamus_DA-lh
+25,accumbens_shell-lh
+26,accumbens_core-lh
+27,pallidum_posterior-lh
+28,pallidum_anterior-lh
+29,putamen_anterior-lh
+30,putamen_posterior-lh
+31,caudate_anterior-lh
+32,caudate_posterior-lh

subcortex_visualization-1.2.0/subcortex_visualization/atlases/Melbourne_S3_subcortex_lookup.csv

@@ -0,0 +1,50 @@
+1,hippocampus_head_med-rh
+2,hippocampus_head_lat-rh
+3,hippocampus_body-rh
+4,hippocampus_tail-rh
+5,thalamus_VP_med-rh
+6,thalamus_VP_lat-rh
+7,thalamus_VA_inf-rh
+8,thalamus_VA_sup-rh
+9,thalamus_DA_med-rh
+10,thalamus_DA_lat-rh
+11,putamen_VA-rh
+12,putamen_DA-rh
+13,putamen_VP-rh
+14,putamen_DP-rh
+15,caudate_VA-rh
+16,caudate_DA-rh
+17,caudate_body-rh
+18,caudate_tail-rh
+19,amygdala_lat-rh
+20,amygdala_med-rh
+21,thalamus_DP-rh
+22,accumbens_shell-rh
+23,accumbens_core-rh
+24,GP_post-rh
+25,GP_ant-rh
+26,hippocampus_head_med-lh
+27,hippocampus_head_lat-lh
+28,hippocampus_body-lh
+29,hippocampus_tail-lh
+30,thalamus_VP_med-lh
+31,thalamus_VP_lat-lh
+32,thalamus_VA_inf-lh
+33,thalamus_VA_sup-lh
+34,thalamus_DA_med-lh
+35,thalamus_DA_lat-lh
+36,putamen_VA-lh
+37,putamen_DA-lh
+38,putamen_VP-lh
+39,putamen_DP-lh
+40,caudate_VA-lh
+41,caudate_DA-lh
+42,caudate_body-lh
+43,caudate_tail-lh
+44,amygdala_lat-lh
+45,amygdala_med-lh
+46,thalamus_DP-lh
+47,accumbens_shell-lh
+48,accumbens_core-lh
+49,GP_post-lh
+50,GP_ant-lh

subcortex_visualization-1.2.0/subcortex_visualization/atlases/Melbourne_S4_subcortex_lookup.csv

@@ -0,0 +1,54 @@
+1,hippocampus_head_med_1-rh
+2,hippocampus_head_med_2-rh
+3,thalamus_VA_inf_post-rh
+4,thalamus_VA_inf_ant-rh
+5,hippocampus_head_lat-rh
+6,hippocampus_body-rh
+7,hippocampus_tail-rh
+8,thalamus_VP_med-rh
+9,thalamus_VP_lat-rh
+10,thalamus_VA_sup-rh
+11,thalamus_DA_med-rh
+12,thalamus_DA_lat-rh
+13,putamen_VA-rh
+14,putamen_DA-rh
+15,putamen_VP-rh
+16,putamen_DP-rh
+17,caudate_VA-rh
+18,caudate_DA-rh
+19,caudate_body-rh
+20,caudate_tail-rh
+21,amygdala_lat-rh
+22,amygdala_med-rh
+23,thalamus_DP-rh
+24,accumbens_shell-rh
+25,accumbens_core-rh
+26,GP_post-rh
+27,GP_ant-rh
+28,hippocampus_head_med_1-lh
+29,hippocampus_head_med_2-lh
+30,thalamus_VA_inf_post-lh
+31,thalamus_VA_inf_ant-lh
+32,hippocampus_head_lat-lh
+33,hippocampus_body-lh
+34,hippocampus_tail-lh
+35,thalamus_VP_med-lh
+36,thalamus_VP_lat-lh
+37,thalamus_VA_sup-lh
+38,thalamus_DA_med-lh
+39,thalamus_DA_lat-lh
+40,putamen_VA-lh
+41,putamen_DA-lh
+42,putamen_VP-lh
+43,putamen_DP-lh
+44,caudate_VA-lh
+45,caudate_DA-lh
+46,caudate_body-lh
+47,caudate_tail-lh
+48,amygdala_lat-lh
+49,amygdala_med-lh
+50,thalamus_DP-lh
+51,accumbens_shell-lh
+52,accumbens_core-lh
+53,GP_post-lh
+54,GP_ant-lh

subcortex_visualization-1.2.0/subcortex_visualization/atlases/SUIT_cerebellar_lobule_lookup.csv

@@ -0,0 +1,28 @@
+1,IV-lh
+2,IV-rh
+3,V-lh
+4,V-rh
+5,VI-lh
+6,VI-vermis
+7,VI-rh
+8,Crus_I-lh
+9,Crus_I-vermis
+10,Crus_I-rh
+11,Crus_II-lh
+12,Crus_II-vermis
+13,Crus_II-rh
+14,VIIb-lh
+15,VIIb-vermis
+16,VIIb-rh
+17,VIIIa-lh
+18,VIIIa-vermis
+19,VIIIa-rh
+20,VIIIb-lh
+21,VIIIb-vermis
+22,VIIIb-rh
+23,IX-lh
+24,IX-vermis
+25,IX-rh
+26,X-lh
+27,X-vermis
+28,X-rh

subcortex_visualization-1.2.0/subcortex_visualization/atlases/Thalamus_Nuclei_HCP_lookup.csv

@@ -0,0 +1,14 @@
+1,Pulvinar-lh
+2,Anterior-lh
+3,Medio_Dorsal-lh
+4,Ventral_Latero_Dorsal-lh
+5,Central_Lateral-Lateral_Posterior-Medial_Pulvinar-lh
+6,Ventral_Anterior-lh
+7,Ventral_Latero_Ventral-lh
+8,Pulvinar-rh
+9,Anterior-rh
+10,Medio_Dorsal-rh
+11,Ventral_Latero_Dorsal-rh
+12,Central_Lateral-Lateral_Posterior-Medial_Pulvinar-rh
+13,Ventral_Anterior-rh
+14,Ventral_Latero_Ventral-rh

subcortex_visualization-1.2.0/subcortex_visualization/atlases/aseg_subcortex_lookup.csv

@@ -0,0 +1,14 @@
+10,thalamus-lh
+11,caudate-lh
+12,putamen-lh
+13,pallidum-lh
+17,hippocampus-lh
+18,amygdala-lh
+26,accumbens-lh
+49,thalamus-rh
+50,caudate-rh
+51,putamen-rh
+52,pallidum-rh
+53,hippocampus-rh
+54,amygdala-rh
+58,accumbens-rh