⚪⚪⚪ Particle Flow Simulator ⚪⚪⚪

This simulator takes a .swc tree graph as input ans outputs 3D particles positions as trajectories and steady state frames.

[Input]

.swc file containing a tree graph with source and target positions with vessel radii

[Output]

Particle Trajectories

Individual 3D particles trajectories in a cell variable stored in a .mat file

Steady State Frames

Temporal frames in a steady state flow (constant amount of particles in time) saved in a .mat file.

Here are the columns signification:

1. Particle ID from the trajectories file
2. Particle position index in it's trajectory from trajectory file
3. Particle X spatial position (um)
4. Particle Y spatial position (um)
5. Particle Z spatial position (um)

Parameters used for previous figure:

1. samp_freq = 1000;
2. n_bubbles = 150000;
3. n_bubbles_steady_state = 5000;
4. t_steady_state = 1;
5. bubble_size = 20;
6. pulsatility = 1;
7. bypass_N_vs_d_stats = 1;

Citing the Particle Flow Simulator

If you use this simulator, please cite:

Peer-reviewed:

• An Anatomically Realistic Simulation Framework for 3D Ultrasound Localization Microscopy, 2023

H. Belgharbi et al., "An Anatomically Realistic Simulation Framework for 3D Ultrasound Localization Microscopy," in IEEE Open Journal of Ultrasonics, Ferroelectrics, and Frequency Control, vol. 3, pp. 1-13, 2023, doi: 10.1109/OJUFFC.2023.3235766.

@ARTICLE{10013486, author={Belgharbi, Hatim and Porée, Jonathan and Damseh, Rafat and Perrot, Vincent and Milecki, Léo and Delafontaine-Martel, Patrick and Lesage, Frédéric and Provost, Jean}, journal={IEEE Open Journal of Ultrasonics, Ferroelectrics, and Frequency Control}, title={An Anatomically Realistic Simulation Framework for 3D Ultrasound Localization Microscopy}, year={2023}, volume={3}, number={}, pages={1-13}, doi={10.1109/OJUFFC.2023.3235766}}

Preprint:

• An Anatomically and Hemodynamically Realistic Simulation Framework for 3D Ultrasound Localization Microscopy, 2021

@article {Belgharbi2021.10.08.463259, author = {Belgharbi, Hatim and Por{'e}e, Jonathan and Damseh, Rafat and Perrot, Vincent and Milecki, L{'e}o and Delafontaine-Martel, Patrick and Lesage, Fr{'e}d{'e}ric and Provost, Jean}, title = {An Anatomically and Hemodynamically Realistic Simulation Framework for 3D Ultrasound Localization Microscopy}, elocation-id = {2021.10.08.463259}, year = {2021}, doi = {10.1101/2021.10.08.463259}, publisher = {Cold Spring Harbor Laboratory}, URL = {https://www.biorxiv.org/content/early/2021/10/09/2021.10.08.463259}, eprint = {https://www.biorxiv.org/content/early/2021/10/09/2021.10.08.463259.full.pdf}, journal = {bioRxiv} }

Related data

If you use the provided data, please cite:

• 3D Simulated Microbubble Flow in a Mouse Vascular Network

@misc{Belgharbi:2022, author = {Belgharbi, Hatim and Porée, Jonathan and Damseh, Rafat and Perrot, Vincent and Milecki, Léo and Delafontaine-Martel, Patrick and Lesage, Frederic and Provost, Jean}, title = {3D Simulated Microbubble Flow in a Mouse Vascular Network}, year = {2022}, howpublished= {10.20383/102.0494} }

Licence

Free software: MIT license