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# brainglobe-heatmap
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Rendering anatomical heatmaps with brainrender and matplotlib.
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`brainglobe-heatmap` allows you to create heatmaps, mapping scalar values for each brain region (e.g., number of labelled cells in each region) to a color and creating beautiful visualizations in 2D (using [matplotlib](https://matplotlib.org/) or 3D (using [brainrender](https://brainglobe.info/documentation/brainrender/index.html)).
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![2D heatmap generated using matplotlib](images/hm_2d.png)
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**2D heatmap generated using matplotlib**
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[![DOI](https://zenodo.org/badge/442271642.svg)](https://zenodo.org/badge/latestdoi/442271642)
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![3D heatmap generated using brainrender](images/hm_3d.png)
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**3D heatmap generated using brainrender**
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`brainglobe-heatmap` makes it easier to create beautiful heatmaps from anatomical data mapping a scalar values for each brain region (e.g., number of labelled cells in each region) to color and creating beautiful visualizations in 3D and 2D.
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![](images/hm_2d.png)
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![](images/hm_3d.png)
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### installation
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## Installation
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`pip install brainglobe-heatmap`
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```
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`brainglobe-heatmap` creates a brainrender 3D `Scene` with the given regions colored according the values in the dictionary.
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Next, to create visualizations like the ones shown above, the three dimensional sceen needs to be **sliced** to expose
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Next, to create visualizations like the ones shown above, the three dimensional scene needs to be **sliced** to expose
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the relevant parts.
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This is done by specifying the position and orientation of a `Plane` which cuts through the scene.
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## Contributing
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Contributions to `brainglobe-heatmap` are more than welcome. Please see the [Developer's guide](https://github.com/brainglobe/.github/blob/main/CONTRIBUTING.md).
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# Citing `brainglobe-heatmap`
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## Citing `brainglobe-heatmap`
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If you use `brainglobe-heatmap` in your work, please cite it as:
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