PyPI - subcortex-visualization - Versions diffs - 1.2.0__tar.gz → 1.2.1__tar.gz - Mend

subcortex-visualization 1.2.0tar.gz → 1.2.1tar.gz

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{subcortex_visualization-1.2.0/subcortex_visualization.egg-info → subcortex_visualization-1.2.1}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: subcortex_visualization
-Version: 1.2.0
+Version: 1.2.1
 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>
@@ -23,9 +23,9 @@ License-File: LICENSE.txt
 Dynamic: author
 Dynamic: license-file
-# Subcortical data visualization in 2D
+# subcortex_visualization: A toolbox for custom data visualization in the subcortex and cerebellum
-[![DOI](https://zenodo.org/badge/965897997.svg)](https://doi.org/10.5281/zenodo.15385315)
+[![DOI:10.64898/2026.01.23.699785](http://img.shields.io/badge/DOI-10.1101/2021.01.08.425840-B31B1B.svg)](https://doi.org/10.64898/2026.01.23.699785)
 This package (implemented in Python and R) currently includes the following nine subcortical and cerebellar atlases for data visualization in two-dimensional vector graphics:
@@ -36,11 +36,11 @@ More information about these atlases, including the process of rendering the sur
 ## 🙋‍♀️ Motivation
 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).
+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) or the [project website page](https://anniegbryant.github.io/subcortex_visualization/custom_segmentation/) 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.
-<img src="docs-site/docs/images/Melbourne_S1_subcortical_atlas_info.png" width="90%">
+<img src="docs-site/docs/images/Melbourne_S1_subcortical_atlas_info.png" width="50%">
 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.
@@ -89,12 +89,12 @@ plot_subcortical_data(hemisphere='L', cmap='plasma',
                       fill_title = "Subcortical region index")
 ```
-<img src="docs-site/docs/images/example_aseg_subcortex_plot.png" width="80%">
+<img src="docs-site/docs/images/example_aseg_subcortex_plot.png" width="60%">
 ### 📚 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).
+For a guide that goes through all the functionality and atlases available in this package, we compiled a simple walkthrough tutorial in Python ([tutorial.ipynb](https://github.com/anniegbryant/subcortex_visualization/blob/main/tutorial.ipynb)) and R ([tutorial_R.md](https://github.com/anniegbryant/subcortex_visualization/blob/main/tutorial_R.md)).
 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  |
@@ -141,11 +141,11 @@ plot_subcortical_data(subcortex_data=example_continuous_data, atlas='aseg',
                       cmap=white_blue_red_cmap, midpoint=0)
 ```
-<img src="docs-site/docs/images/example_aseg_subcortex_normdist.png" width="80%">
+<img src="docs-site/docs/images/example_aseg_subcortex_normdist.png" width="75%">
-### Available atlases
+### 🗺️ Available atlases
-The following nine subcortical atlases are currently supported with more information at the [project website](https://anniegbryant.github.io/subcortex_visualization/atlas_info/):
+The following subcortical and cerebellar 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)
@@ -157,10 +157,17 @@ The following nine subcortical atlases are currently supported with more informa
 * `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)
+### 🌟 Atlas wishlist
+These atlases are on the 'vision board' for me to add to the package next (community pull requests absolutely welcome to incorporate these in the meantime):
+* Thalamus-Optimized Multi-Atlas Segmentation (THOMAS) atlas: High-resolution segmentation of thalamic nuclei ([file link](https://zenodo.org/records/5499504)), recently expanded to all deep grey nuclei as described in [Saranathan et al. (2025)](https://doi.org/10.1002/hbm.70350)
+* Brainstem (suggested by [@RaviBot](https://github.com/RaviBot)): Brainstem Navigator atlas ([file link](https://www.nitrc.org/projects/brainstemnavig)), as described in [Bianciardi et al. (2015)](https://doi.org/10.1089/brain.2015.0347)
+* CIT168 Reinforcement Learning Atlas (suggested by [@GalKepler](https://github.com/GalKepler)): Subcortical atlas ([file link](https://osf.io/jkzwp/wiki)) that includes the principal nuclei involved in reinforcement learning, as described in [Pauli et al. (2018)](https://doi.org/10.1038/sdata.2018.63)
 ## 💡 Want to generate your own mesh and/or parcellation?
-<img src="docs-site/docs/images/custom_vector_method.png" width="70%">
+<img src="docs-site/docs/images/custom_vector_method.png" width="60%">
 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!
@@ -168,21 +175,39 @@ We have a dedicated folder for a custom segmentation pipeline that will walk you
 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.
+Check out the walkthrough in the [`custom_segmentation/`](https://github.com/anniegbryant/subcortex_visualization/tree/main/custom_segmentation) folder or the [project website page](https://anniegbryant.github.io/subcortex_visualization/custom_segmentation/) 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
+## 🔗 Citing this package
-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!
+If you use this package in a scientific publication, blog post, etc., please read and cite the [associated preprint](https://www.biorxiv.org/content/10.64898/2026.01.23.699785):
-We're also very grateful for ongoing contributions from members of the GitHub community:
+* 📕 Bryant, Annie G. (2026). Subcortex visualization: A toolbox for custom data visualization in the subcortex and cerebellum. *bioRxiv*, 2026-01. doi:10.64898/2026.01.23.699785.
-[![Contributors](https://contrib.rocks/image?repo=anniegbryant/subcortex_visualization)](https://github.com/anniegbryant/subcortex_visualization/graphs/contributors)
+<details closed>
+    <summary>Click here for a BibTex reference:</summary>
-## 🔗 Citing this package
+```
+@article{bryant2026subcortex,
+	title = {Subcortex visualization: A toolbox for custom data visualization in the subcortex and cerebellum},
+	url = {https://www.biorxiv.org/content/10.64898/2026.01.23.699785},
+	doi = {10.64898/2026.01.23.699785},
+	journal = {bioRxiv},
+  publisher={Cold Spring Harbor Laboratory},
+	author = {Bryant, Annie G.},
+  pages = {2026--01},
+	year = {2026}
+}
+```
+</details>
+## 🙏 Acknowledgments
-If you use this package in a scientific publication, blog post, etc., please cite the corresponding Zenodo release as follows:
+Thank you very much to [Sidhant Chopra](https://github.com/sidchop), [Chris Rorden](https://github.com/rordenlab), [Justine Hansen](https://github.com/justinehansen), and [Ye Tian](https://github.com/yetianmed) for their suggestions and continued development of open tools for neuroimaging visualization that enabled the development of this project!
-Annie G. Bryant. (2025). anniegbryant/subcortex_visualization: Initial Zenodo release (initial_release). Zenodo. https://doi.org/10.5281/zenodo.15385316
+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)
 ## ❓📧 Questions, comments, or suggestions always welcome!

{subcortex_visualization-1.2.0 → subcortex_visualization-1.2.1}/README.md RENAMED Viewed

@@ -1,6 +1,6 @@
-# Subcortical data visualization in 2D
+# subcortex_visualization: A toolbox for custom data visualization in the subcortex and cerebellum
-[![DOI](https://zenodo.org/badge/965897997.svg)](https://doi.org/10.5281/zenodo.15385315)
+[![DOI:10.64898/2026.01.23.699785](http://img.shields.io/badge/DOI-10.1101/2021.01.08.425840-B31B1B.svg)](https://doi.org/10.64898/2026.01.23.699785)
 This package (implemented in Python and R) currently includes the following nine subcortical and cerebellar atlases for data visualization in two-dimensional vector graphics:
@@ -11,11 +11,11 @@ More information about these atlases, including the process of rendering the sur
 ## 🙋‍♀️ Motivation
 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).
+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) or the [project website page](https://anniegbryant.github.io/subcortex_visualization/custom_segmentation/) 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.
-<img src="docs-site/docs/images/Melbourne_S1_subcortical_atlas_info.png" width="90%">
+<img src="docs-site/docs/images/Melbourne_S1_subcortical_atlas_info.png" width="50%">
 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.
@@ -64,12 +64,12 @@ plot_subcortical_data(hemisphere='L', cmap='plasma',
                       fill_title = "Subcortical region index")
 ```
-<img src="docs-site/docs/images/example_aseg_subcortex_plot.png" width="80%">
+<img src="docs-site/docs/images/example_aseg_subcortex_plot.png" width="60%">
 ### 📚 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).
+For a guide that goes through all the functionality and atlases available in this package, we compiled a simple walkthrough tutorial in Python ([tutorial.ipynb](https://github.com/anniegbryant/subcortex_visualization/blob/main/tutorial.ipynb)) and R ([tutorial_R.md](https://github.com/anniegbryant/subcortex_visualization/blob/main/tutorial_R.md)).
 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  |
@@ -116,11 +116,11 @@ plot_subcortical_data(subcortex_data=example_continuous_data, atlas='aseg',
                       cmap=white_blue_red_cmap, midpoint=0)
 ```
-<img src="docs-site/docs/images/example_aseg_subcortex_normdist.png" width="80%">
+<img src="docs-site/docs/images/example_aseg_subcortex_normdist.png" width="75%">
-### Available atlases
+### 🗺️ Available atlases
-The following nine subcortical atlases are currently supported with more information at the [project website](https://anniegbryant.github.io/subcortex_visualization/atlas_info/):
+The following subcortical and cerebellar 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)
@@ -132,10 +132,17 @@ The following nine subcortical atlases are currently supported with more informa
 * `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)
+### 🌟 Atlas wishlist
+These atlases are on the 'vision board' for me to add to the package next (community pull requests absolutely welcome to incorporate these in the meantime):
+* Thalamus-Optimized Multi-Atlas Segmentation (THOMAS) atlas: High-resolution segmentation of thalamic nuclei ([file link](https://zenodo.org/records/5499504)), recently expanded to all deep grey nuclei as described in [Saranathan et al. (2025)](https://doi.org/10.1002/hbm.70350)
+* Brainstem (suggested by [@RaviBot](https://github.com/RaviBot)): Brainstem Navigator atlas ([file link](https://www.nitrc.org/projects/brainstemnavig)), as described in [Bianciardi et al. (2015)](https://doi.org/10.1089/brain.2015.0347)
+* CIT168 Reinforcement Learning Atlas (suggested by [@GalKepler](https://github.com/GalKepler)): Subcortical atlas ([file link](https://osf.io/jkzwp/wiki)) that includes the principal nuclei involved in reinforcement learning, as described in [Pauli et al. (2018)](https://doi.org/10.1038/sdata.2018.63)
 ## 💡 Want to generate your own mesh and/or parcellation?
-<img src="docs-site/docs/images/custom_vector_method.png" width="70%">
+<img src="docs-site/docs/images/custom_vector_method.png" width="60%">
 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!
@@ -143,21 +150,39 @@ We have a dedicated folder for a custom segmentation pipeline that will walk you
 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.
+Check out the walkthrough in the [`custom_segmentation/`](https://github.com/anniegbryant/subcortex_visualization/tree/main/custom_segmentation) folder or the [project website page](https://anniegbryant.github.io/subcortex_visualization/custom_segmentation/) 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
+## 🔗 Citing this package
-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!
+If you use this package in a scientific publication, blog post, etc., please read and cite the [associated preprint](https://www.biorxiv.org/content/10.64898/2026.01.23.699785):
-We're also very grateful for ongoing contributions from members of the GitHub community:
+* 📕 Bryant, Annie G. (2026). Subcortex visualization: A toolbox for custom data visualization in the subcortex and cerebellum. *bioRxiv*, 2026-01. doi:10.64898/2026.01.23.699785.
-[![Contributors](https://contrib.rocks/image?repo=anniegbryant/subcortex_visualization)](https://github.com/anniegbryant/subcortex_visualization/graphs/contributors)
+<details closed>
+    <summary>Click here for a BibTex reference:</summary>
-## 🔗 Citing this package
+```
+@article{bryant2026subcortex,
+	title = {Subcortex visualization: A toolbox for custom data visualization in the subcortex and cerebellum},
+	url = {https://www.biorxiv.org/content/10.64898/2026.01.23.699785},
+	doi = {10.64898/2026.01.23.699785},
+	journal = {bioRxiv},
+  publisher={Cold Spring Harbor Laboratory},
+	author = {Bryant, Annie G.},
+  pages = {2026--01},
+	year = {2026}
+}
+```
+</details>
+## 🙏 Acknowledgments
-If you use this package in a scientific publication, blog post, etc., please cite the corresponding Zenodo release as follows:
+Thank you very much to [Sidhant Chopra](https://github.com/sidchop), [Chris Rorden](https://github.com/rordenlab), [Justine Hansen](https://github.com/justinehansen), and [Ye Tian](https://github.com/yetianmed) for their suggestions and continued development of open tools for neuroimaging visualization that enabled the development of this project!
-Annie G. Bryant. (2025). anniegbryant/subcortex_visualization: Initial Zenodo release (initial_release). Zenodo. https://doi.org/10.5281/zenodo.15385316
+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)
 ## ❓📧 Questions, comments, or suggestions always welcome!

{subcortex_visualization-1.2.0 → subcortex_visualization-1.2.1}/pyproject.toml RENAMED Viewed

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "subcortex_visualization"
-version = "1.2.0"
+version = "1.2.1"
 authors = [
   { name="Annie G. Bryant", email="anniegbryant@gmail.com" },
 ]

{subcortex_visualization-1.2.0 → subcortex_visualization-1.2.1}/setup.py RENAMED Viewed

@@ -10,7 +10,7 @@ install_requires = [
 setup(
     name='subcortex_visualization',
-    version='1.2.0',
+    version='1.2.1',
     description='Visualize subcortical brain data from SVG templates',
     author='Annie G. Bryant',
     packages=find_packages(),

{subcortex_visualization-1.2.0 → subcortex_visualization-1.2.1}/subcortex_visualization/segmentation.py RENAMED Viewed

@@ -3,14 +3,14 @@ import os
 import numpy as np
 import pandas as pd
-# Imaging masker
-from nilearn.maskers import NiftiLabelsMasker
+# neuromaps imports
+from neuromaps.parcellate import Parcellater
 # Files
 from importlib.resources import files
 def apply_atlas_to_data(functional_map, atlas, func_name='Functional map'):
-    """Apply subcortical atlas to functional map and extract mean signal per region.
+    """Apply subcortical atlas(es) to a given functional map and extract mean signal per region.
     Parameters
     ----------
     functional_map : str or Nifti1Image
@@ -45,18 +45,9 @@ def apply_atlas_to_data(functional_map, atlas, func_name='Functional map'):
         this_atlas_LUT = pd.read_csv(files("subcortex_visualization.atlases").joinpath(f"{this_atlas_file}_lookup.csv"), header=None)
         this_atlas_LUT.columns = ['Index', 'Region']
-        # Apply example_seg to example_functional_map
-        masker = NiftiLabelsMasker(
-            labels_img=this_atlas_volume_path,
-            memory="nilearn_cache",
-            standardize=False
-        )
-        # Apply masker to functional map
-        functional_map_parc = masker.fit_transform(functional_map)
-        # Make sure the results are one-column
-        functional_map_parc = functional_map_parc.flatten()
+        # Use the Parcellator object from neuromaps to apply the atlas to the functional map
+        parcellator = Parcellater(this_atlas_volume_path, 'MNI152')
+        functional_map_parc = parcellator.fit_transform(functional_map, 'MNI152', True).squeeze()
         # Merge region and index
         functional_map_parc_df = pd.DataFrame({'Functional_Map': func_name,

subcortex_visualization-1.2.1/subcortex_visualization/utils.py ADDED Viewed

@@ -0,0 +1,45 @@
+# Necessary imports
+import pandas as pd
+import numpy as np
+# Files
+from importlib.resources import files
+def get_atlas_regions(atlas_name):
+    """Print the names of regions in a given subcortical/cerebellar atlas.
+    Parameters
+    ----------
+    atlas_name : str
+        Name of the subcortical/cerebellar atlas.
+    Returns
+    -------
+    np.ndarray
+        Array of region names in the specified atlas, ordered by segmentation index.
+    """
+    # If the atlas is the SUIT cerebellar lobules, use hemisphere of 'both'
+    if atlas_name == 'SUIT_cerebellar_lobule':
+        hemisphere = 'both'
+        # Load ordering file
+        atlas_ordering = pd.read_csv(files("subcortex_visualization.data").joinpath(f"{atlas_name}_{hemisphere}_ordering.csv"))
+        # Identify regions for left/right cerebellar cortex versus vermis
+        hemisphere_regions = atlas_ordering.query("Hemisphere == 'L'").sort_values('seg_index').region.unique()
+        vermis_regions = atlas_ordering.query("Hemisphere=='V'").sort_values('seg_index').region.unique()
+        # Return both lists of regions as a tuple
+        return (hemisphere_regions, vermis_regions)
+    # Else, use left hemisphere just to get names
+    else:
+        hemisphere='L'
+        # Load ordering file
+        atlas_ordering = pd.read_csv(files("subcortex_visualization.data").joinpath(f"{atlas_name}_{hemisphere}_ordering.csv"))
+        # Sort by segmentation index and print the array of region names
+        unique_regions = atlas_ordering.sort_values('seg_index').region.unique()
+        return unique_regions

{subcortex_visualization-1.2.0 → subcortex_visualization-1.2.1/subcortex_visualization.egg-info}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: subcortex_visualization
-Version: 1.2.0
+Version: 1.2.1
 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>
@@ -23,9 +23,9 @@ License-File: LICENSE.txt
 Dynamic: author
 Dynamic: license-file
-# Subcortical data visualization in 2D
+# subcortex_visualization: A toolbox for custom data visualization in the subcortex and cerebellum
-[![DOI](https://zenodo.org/badge/965897997.svg)](https://doi.org/10.5281/zenodo.15385315)
+[![DOI:10.64898/2026.01.23.699785](http://img.shields.io/badge/DOI-10.1101/2021.01.08.425840-B31B1B.svg)](https://doi.org/10.64898/2026.01.23.699785)
 This package (implemented in Python and R) currently includes the following nine subcortical and cerebellar atlases for data visualization in two-dimensional vector graphics:
@@ -36,11 +36,11 @@ More information about these atlases, including the process of rendering the sur
 ## 🙋‍♀️ Motivation
 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).
+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) or the [project website page](https://anniegbryant.github.io/subcortex_visualization/custom_segmentation/) 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.
-<img src="docs-site/docs/images/Melbourne_S1_subcortical_atlas_info.png" width="90%">
+<img src="docs-site/docs/images/Melbourne_S1_subcortical_atlas_info.png" width="50%">
 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.
@@ -89,12 +89,12 @@ plot_subcortical_data(hemisphere='L', cmap='plasma',
                       fill_title = "Subcortical region index")
 ```
-<img src="docs-site/docs/images/example_aseg_subcortex_plot.png" width="80%">
+<img src="docs-site/docs/images/example_aseg_subcortex_plot.png" width="60%">
 ### 📚 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).
+For a guide that goes through all the functionality and atlases available in this package, we compiled a simple walkthrough tutorial in Python ([tutorial.ipynb](https://github.com/anniegbryant/subcortex_visualization/blob/main/tutorial.ipynb)) and R ([tutorial_R.md](https://github.com/anniegbryant/subcortex_visualization/blob/main/tutorial_R.md)).
 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  |
@@ -141,11 +141,11 @@ plot_subcortical_data(subcortex_data=example_continuous_data, atlas='aseg',
                       cmap=white_blue_red_cmap, midpoint=0)
 ```
-<img src="docs-site/docs/images/example_aseg_subcortex_normdist.png" width="80%">
+<img src="docs-site/docs/images/example_aseg_subcortex_normdist.png" width="75%">
-### Available atlases
+### 🗺️ Available atlases
-The following nine subcortical atlases are currently supported with more information at the [project website](https://anniegbryant.github.io/subcortex_visualization/atlas_info/):
+The following subcortical and cerebellar 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)
@@ -157,10 +157,17 @@ The following nine subcortical atlases are currently supported with more informa
 * `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)
+### 🌟 Atlas wishlist
+These atlases are on the 'vision board' for me to add to the package next (community pull requests absolutely welcome to incorporate these in the meantime):
+* Thalamus-Optimized Multi-Atlas Segmentation (THOMAS) atlas: High-resolution segmentation of thalamic nuclei ([file link](https://zenodo.org/records/5499504)), recently expanded to all deep grey nuclei as described in [Saranathan et al. (2025)](https://doi.org/10.1002/hbm.70350)
+* Brainstem (suggested by [@RaviBot](https://github.com/RaviBot)): Brainstem Navigator atlas ([file link](https://www.nitrc.org/projects/brainstemnavig)), as described in [Bianciardi et al. (2015)](https://doi.org/10.1089/brain.2015.0347)
+* CIT168 Reinforcement Learning Atlas (suggested by [@GalKepler](https://github.com/GalKepler)): Subcortical atlas ([file link](https://osf.io/jkzwp/wiki)) that includes the principal nuclei involved in reinforcement learning, as described in [Pauli et al. (2018)](https://doi.org/10.1038/sdata.2018.63)
 ## 💡 Want to generate your own mesh and/or parcellation?
-<img src="docs-site/docs/images/custom_vector_method.png" width="70%">
+<img src="docs-site/docs/images/custom_vector_method.png" width="60%">
 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!
@@ -168,21 +175,39 @@ We have a dedicated folder for a custom segmentation pipeline that will walk you
 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.
+Check out the walkthrough in the [`custom_segmentation/`](https://github.com/anniegbryant/subcortex_visualization/tree/main/custom_segmentation) folder or the [project website page](https://anniegbryant.github.io/subcortex_visualization/custom_segmentation/) 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
+## 🔗 Citing this package
-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!
+If you use this package in a scientific publication, blog post, etc., please read and cite the [associated preprint](https://www.biorxiv.org/content/10.64898/2026.01.23.699785):
-We're also very grateful for ongoing contributions from members of the GitHub community:
+* 📕 Bryant, Annie G. (2026). Subcortex visualization: A toolbox for custom data visualization in the subcortex and cerebellum. *bioRxiv*, 2026-01. doi:10.64898/2026.01.23.699785.
-[![Contributors](https://contrib.rocks/image?repo=anniegbryant/subcortex_visualization)](https://github.com/anniegbryant/subcortex_visualization/graphs/contributors)
+<details closed>
+    <summary>Click here for a BibTex reference:</summary>
-## 🔗 Citing this package
+```
+@article{bryant2026subcortex,
+	title = {Subcortex visualization: A toolbox for custom data visualization in the subcortex and cerebellum},
+	url = {https://www.biorxiv.org/content/10.64898/2026.01.23.699785},
+	doi = {10.64898/2026.01.23.699785},
+	journal = {bioRxiv},
+  publisher={Cold Spring Harbor Laboratory},
+	author = {Bryant, Annie G.},
+  pages = {2026--01},
+	year = {2026}
+}
+```
+</details>
+## 🙏 Acknowledgments
-If you use this package in a scientific publication, blog post, etc., please cite the corresponding Zenodo release as follows:
+Thank you very much to [Sidhant Chopra](https://github.com/sidchop), [Chris Rorden](https://github.com/rordenlab), [Justine Hansen](https://github.com/justinehansen), and [Ye Tian](https://github.com/yetianmed) for their suggestions and continued development of open tools for neuroimaging visualization that enabled the development of this project!
-Annie G. Bryant. (2025). anniegbryant/subcortex_visualization: Initial Zenodo release (initial_release). Zenodo. https://doi.org/10.5281/zenodo.15385316
+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)
 ## ❓📧 Questions, comments, or suggestions always welcome!

subcortex_visualization-1.2.0/subcortex_visualization/utils.py DELETED Viewed

@@ -1,20 +0,0 @@
-# Necessary imports
-import pandas as pd
-import numpy as np
-# Files
-from importlib.resources import files
-def get_atlas_regions(atlas_name):
-    # Use left hemisphere just to get names
-    hemisphere='L'
-    # Load ordering file
-    atlas_ordering = pd.read_csv(files("subcortex_visualization.data").joinpath(f"{atlas_name}_{hemisphere}_ordering.csv"))
-    # Sort by segmentation index and print the array of region names
-    unique_regions = atlas_ordering.sort_values('seg_index').region.unique()
-    return unique_regions