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:

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:

from vascpy import PointVasculature

v = PointVasculature.load_sonata("sample_sonata.h5")

print(v.node_properties)
print(v.edge_properties)
print(v.points)
print(v.edges)
print(v.edge_types)
print(v.segment_points)
print(v.segment_diameters)
print(v.area)
print(v.volume)

v.save_sonata("sample_sonata2.h5")

Representation conversions

vascpy allows the conversion between the two representations:

from vascpy import PointVasculature
point_vasculature = PointVasculature.load_hdf5("sample_sonata.h5")

section_vasculature = point_vasculature.as_section_graph()
point_vasculature = section_vasculature.as_point_graph()

Create and save an edge-centered vascular graph

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])
})

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

v = PointVasculature(node_properties=node_properties, edge_properties=edge_properties)
v.save_sonata('my_vasculature.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