[!WARNING] The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization. Future development will take place at: https://github.com/openbraininstitute/vascpy

vascpy

vascpy is a python library for reading, writing, and manipulating large-scale vasculature graphs. There are two alternative graph representations available: a section-centered and an edge-centered one. It supports the following respective formats:

• H5 Morphology (see specification)
• SONATA node population of edges (see specification)

The vascpy library provides two classes: PointVasculature and SectionVasculature that allow for reading and writing edge-centered and section-centered datasets respectively, as well as converting between them.

Documentation

vascpy documentation is built and hosted on readthedocs. * latest snapshot

Usage

Load and write an h5 morphology file:

```python from vascpy import SectionVasculature

v = SectionVasculature.load("sample.h5")

print(v.points) print(v.diameters) print(v.connectivity) print(v.sections)

v.save("sample2.h5") ```

Load and write an h5 SONATA file: ```python from vascpy import PointVasculature

v = PointVasculature.loadsonata("samplesonata.h5")

print(v.nodeproperties) print(v.edgeproperties) print(v.points) print(v.edges) print(v.edgetypes) print(v.segmentpoints) print(v.segment_diameters) print(v.area) print(v.volume)

v.savesonata("samplesonata2.h5") ```

Representation conversions

vascpy allows the conversion between the two representations:

```python from vascpy import PointVasculature pointvasculature = PointVasculature.loadhdf5("sample_sonata.h5")

sectionvasculature = pointvasculature.assectiongraph() pointvasculature = sectionvasculature.aspointgraph() ```

Create and save an edge-centered vascular graph

```python import numpy as np import pandas as pd from vascpy import PointVasculature

node_properties = DataFrame({ 'x': np.array([0., 1., 2.]), 'y': np.array([3., 4., 5.]), 'z': np.array([6., 7., 8.]), 'diameter': np.array([0.1, 0.2, 0.3]) })

edgeproperties = pd.DataFrame({ 'startnode': np.array([0, 0, 1]), 'end_node': np.array([1, 2, 2]), 'type': np.array([1, 1, 1]) })

v = PointVasculature(nodeproperties=nodeproperties, edgeproperties=edgeproperties) v.savesonata('myvasculature.h5') ```

Funding & Acknowledgements

The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.

Copyright (c) 2022-2024 Blue Brain Project/EPFL