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README.md

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@@ -47,11 +47,21 @@ cardiotensor's documentation is available at [josephbrunet.fr/cardiotensor/](htt
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Have a look at our [simple example](https://www.josephbrunet.fr/cardiotensor/getting-started/examples/) that runs you through all the commands of the package
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<p align="center">
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<img src="https://github.com/JosephBrunet/cardiotensor/raw/main/assets/images/pipeline.png" alt="Example Slice" style="max-width: 70%">
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<img src="https://github.com/JosephBrunet/cardiotensor/raw/main/assets/images/pipeline.png"
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alt="Cardiotensor pipeline for 3D cardiac orientation analysis"
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style="max-width: 100%; border-radius: 6px;">
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<br>
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<em>Helical angle map of a heart scanned using synchrtron X-ray imaging.</em>
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<em>
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<strong>Overview of the <code>cardiotensor</code> pipeline for 3D cardiac orientation analysis and tractography.</strong>
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<strong>(a)</strong> Input data consist of a whole‑ or partial‑heart volume and, optionally, a binary mask to restrict analysis to myocardial tissue.
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<strong>(b)</strong> Local cardiomyocyte orientation is derived by 3D structure tensor computation and eigenvector decomposition.
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The third eigenvector (smallest eigenvalue) is visualized as arrows, color‑coded by helix angle (HA); inset shows a zoom of the ventricular septum highlighting transmural fiber rotation.
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<strong>(c)</strong> After transforming to a cylindrical coordinate system aligned with the left ventricle, voxel‑wise HA, transverse angle (TA), and fractional anisotropy (FA) maps are computed for quantitative analysis.
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<strong>(d)</strong> Streamline tractography generated from the eigenvector field reveals continuous cardiomyocyte bundles throughout the heart, color‑coded by HA.
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</em>
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</p>
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## More Information
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This package uses the [structure-tensor](https://github.com/Skielex/structure-tensor) package to calculate the structure tensor, extending its capabilities for cardiac imaging.

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