Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/neuro-mechatronics-interfaces/python_ultrasound_reconstruction
A Python library for 3D free-hand ultra-sound measurements, volumetric reconstruction, and segmentation
https://github.com/neuro-mechatronics-interfaces/python_ultrasound_reconstruction
Last synced: 24 days ago
JSON representation
A Python library for 3D free-hand ultra-sound measurements, volumetric reconstruction, and segmentation
- Host: GitHub
- URL: https://github.com/neuro-mechatronics-interfaces/python_ultrasound_reconstruction
- Owner: Neuro-Mechatronics-Interfaces
- License: gpl-3.0
- Created: 2024-07-03T20:28:02.000Z (7 months ago)
- Default Branch: main
- Last Pushed: 2024-07-26T15:44:12.000Z (6 months ago)
- Last Synced: 2024-07-26T21:54:10.984Z (6 months ago)
- Language: Python
- Size: 17.9 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# 3D multimodal medical imaging technique based on freehand ultrasound, marker tracking, and 3D reconstruction
This is the main repository for the Python3-based 3D multimodal imaging technique using freehand ultrasound and marker tracking. The project is a part of the Neuro-Mechatronics Interfaces group at Carnegie Mellon University
With this proposed technique, we can obtain the internal structure with 3D freehand ultrasound to complement the design process of an HD-EMG sleeve with optimized electrode positioning. Our system is composed of 8 Vicon tracking cameras and an ultrasound machine.
This project is inspired by [Jhacson Meza](https://jhacsonmeza.github.io/)'s work on [3D ultrasound reconstruction](https://arxiv.org/abs/2105.14355)
Note: This process assumes that the motion tracking data contains at least 3 markers on a plane to be able to reconstruct the pose of the ultrasound probe. The motion tracking data should be in the form of a CSV file with the following format:
## Dependencies
* [Python 3.8](https://www.python.org/downloads/)
* [Vicon Nexus 2.11](https://www.vicon.com/software/nexus/)
## Repository Structure
The following demonstrates the structure as well as useage of the folders and files:
* `dataset/` - The primary directory containing the generated data
* `models/` - The directory containing STL files used in visualization
* `1_process_us_video.py` - The script to process the ultrasound video
* `2_pose_estimation.py` - Loads motion tracking data and estimates the pose of the ultrasound probe
* `3_multimodal_alignment.py` - Aligns the ultrasound and motion tracking data using correlation tecnique
* `4_reconstruction.py` - Generates the 3D reconstruction of the ultrasound data
## Installation
To get started, clone the repository and navigate to the package directory:
```
git clone https://github.com/Neuro-Mechatronics-Interfaces/Python_Ultrasound_Reconstruction.git
cd Python_Ultrasound_Recunstruction
```
- (Optional) Installing packages locally in a virtual environment instead of the PC is optional but recommended:
```
python -m venv py_us
```
- Activate the new environment:
```
# In cmd.exe
py_us\Scripts\activate.bat
# In PowerShell
py_us\Scripts\Activate.ps1
# On Linux and MacOS
source py_us/bin/activate
```
- When you're done, to deactivate the virtual environment, you can run the `deactivate` command:
```
deactivate
```
Install the python packages required for the project in the environment:
```
pip install -r requirements.txt
```
- If it fails, try upgrading your pip version:
```
python -m pip install --upgrade pip
```
## Usage
Set the path to the dataset in the `1_process_us_video.py` script and run the script to process the ultrasound video:
```
python 1_process_us_video.py
```
Set the path to the dataset in the `2_pose_estimation.py` script and run the script to estimate the pose of the ultrasound probe:
```
python 2_pose_estimation.py
```
Set the path to the dataset in the `3_multimodal_alignment.py` script and run the script to align the ultrasound and motion tracking data:
```
python 3_multimodal_alignment.py
```
Set the path to the dataset in the `4_reconstruction.py` script and run the script to generate the 3D reconstruction of the ultrasound data:
```
python 4_reconstruction.py
```
## Citation