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https://github.com/ad12/meddlr
A flexible ML framework built to simplify medical image reconstruction and analysis experimentation.
https://github.com/ad12/meddlr
inverse-problems machine-learning medical-imaging mri
Last synced: about 20 hours ago
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A flexible ML framework built to simplify medical image reconstruction and analysis experimentation.
- Host: GitHub
- URL: https://github.com/ad12/meddlr
- Owner: ad12
- License: apache-2.0
- Created: 2021-11-02T21:45:16.000Z (about 3 years ago)
- Default Branch: main
- Last Pushed: 2024-12-09T06:30:51.000Z (about 1 month ago)
- Last Synced: 2025-01-02T07:07:23.133Z (8 days ago)
- Topics: inverse-problems, machine-learning, medical-imaging, mri
- Language: Python
- Homepage:
- Size: 8.23 MB
- Stars: 62
- Watchers: 3
- Forks: 15
- Open Issues: 9
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
# meddlr
[](https://meddlr.readthedocs.io/en/latest/?badge=latest)
[](https://github.com/pre-commit/pre-commit)
[](https://codecov.io/gh/ad12/meddlr)
[Getting Started](GETTING_STARTED.md)
Meddlr is a config-driven ML framework built to simplify medical image reconstruction and analysis problems.
## ⚡ QuickStart
```bash
# Install Meddlr with basic dependencies
pip install meddlr
# Install Meddlr with all dependencies (e.g. pretrained models, benchmarking)
pip install 'meddlr[all]'
```
> _Installing locally_: For local development, fork and clone the repo and run `pip install -e ".[alldev]"`
> _Installing from main_: For most up-to-date code without a local install, run `pip install "meddlr @ git+https://github.com/ad12/meddlr@main"`
Configure your paths and get going!
```python
import meddlr as mr
import os
# (Optional) Configure and save machine/cluster preferences.
# This only has to be done once and will persist across sessions.
cluster = mr.Cluster()
cluster.set(results_dir="/path/to/save/results", data_dir="/path/to/datasets")
cluster.save()
# OR set these as environment variables.
os.environ["MEDDLR_RESULTS_DIR"] = "/path/to/save/results"
os.environ["MEDDLR_DATASETS_DIR"] = "/path/to/datasets"
```
Detailed instructions are available in [Getting Started](GETTING_STARTED.md).
## Visualizations
Use [MeddlrViz](https://github.com/ad12/meddlr-viz) to visualize your medical imaging datasets, ML models, and more!
```bash
pip install meddlr-viz
```
## 🐘 Model Zoo
Easily serve and download pretrained models from the model zoo. A (evolving) list of pre-trained models can be found [here](MODEL_ZOO.md), on [HuggingFace 🤗](https://huggingface.co/arjundd), and in [project folders](projects).
To use them, pass the URLs for the config and weights (model) files to `mr.get_model_from_zoo`:
```python
import meddlr as mr
model = mr.get_model_from_zoo(
cfg_or_file="https://huggingface.co/arjundd/vortex-release/resolve/main/mridata_knee_3dfse/Supervised/config.yaml",
weights_path="https://huggingface.co/arjundd/vortex-release/resolve/main/mridata_knee_3dfse/Supervised/model.ckpt",
)
```
## 📓 Projects
Check out some [projects](projects) built with meddlr!
## ✏️ Contributing
Want to add new features, fix a bug, or add your project? We'd love to include them! See [CONTRIBUTING.md](CONTRIBUTING.md) for more information.
## Acknowledgements
Meddlr's design for rapid experimentation and benchmarking is inspired by [detectron2](https://github.com/facebookresearch/detectron2).
## About
If you use Meddlr for your work, please consider citing the following work:
```
@article{desai2021noise2recon,
title={Noise2Recon: A Semi-Supervised Framework for Joint MRI Reconstruction and Denoising},
author={Desai, Arjun D and Ozturkler, Batu M and Sandino, Christopher M and Vasanawala, Shreyas and Hargreaves, Brian A and Re, Christopher M and Pauly, John M and Chaudhari, Akshay S},
journal={arXiv preprint arXiv:2110.00075},
year={2021}
}
```