fUSI vascular template from Huang et al., 2025

Export a ConfUSIus-loadable vascular template aligned to the Allen atlas from the published OpenfUSAnalyzer (OfUSA) mouse atlas template.

Source dataset

The input template used here comes from:

• Huang, Y.-A. et al. (2025). OfUSA: OpenfUS Analyzer, a versatile open-source framework for the analysis and visualization of functional ultrasound imaging data across animal models. DOI: 10.1101/2025.09.16.676515.

The source template data is distributed under CC BY-NC-SA 4.0. The exported template in this project is a transformed derivative and should be reused under compatible terms with attribution.

Inputs

This repository contains the input file required to build the exported template:

• inputs/OFUSA_Atlas_Mouse_Vascular.nii

Transform

template = cf.load(...)
atlas = cf.atlas.Atlas.from_brainglobe("allen_mouse_50um")
template = template.rename({"x": "y", "y": "z", "z": "x"}).transpose("z", "y", "x").assign_coords(atlas.reference.coords)

Output

Running the export writes:

• outputs/huang-2025-space-allen50_desc-vascular.nii.gz

Usage

Export the template:

uv run main.py

Use it later with ConfUSIus:

import confusius as cf
from confusius.atlas.atlas import Atlas

template = cf.load("outputs/huang-2025-space-allen50_desc-vascular.nii.gz")
atlas = Atlas.from_brainglobe("allen_mouse_50um")

Licensing

• Code license: BSD-3-Clause (LICENSE)
• Data license: CC BY-NC-SA 4.0 (licenses/DATA_LICENSE.md)

Citation notes

At minimum cite:

1. Huang et al. (2025) / OpenfUSAnalyzer for the vascular template.
2. Wang et al. (2020) for the Allen CCF reference framework.