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meddlr\n![GitHub Workflow Status](https://img.shields.io/github/workflow/status/ad12/meddlr/CI)\n![GitHub](https://img.shields.io/github/license/ad12/meddlr)\n[![Documentation Status](https://readthedocs.org/projects/meddlr/badge/?version=latest)](https://meddlr.readthedocs.io/en/latest/?badge=latest)\n[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit\u0026logoColor=white)](https://github.com/pre-commit/pre-commit)\n[![codecov](https://codecov.io/gh/ad12/meddlr/branch/main/graph/badge.svg?token=U6H83UCGFU)](https://codecov.io/gh/ad12/meddlr)\n\n[Getting Started](GETTING_STARTED.md)\n\nMeddlr is a config-driven ML framework built to simplify medical image reconstruction and analysis problems.\n\n## ⚡ QuickStart\n```bash\n# Install Meddlr with basic dependencies\npip install meddlr\n\n# Install Meddlr with all dependencies (e.g. pretrained models, benchmarking)\npip install 'meddlr[all]'\n```\n\n\u003e _Installing locally_: For local development, fork and clone the repo and run `pip install -e \".[alldev]\"`\n\n\u003e _Installing from main_: For most up-to-date code without a local install, run `pip install \"meddlr @ git+https://github.com/ad12/meddlr@main\"`\n\nConfigure your paths and get going!\n```python\nimport meddlr as mr\nimport os\n\n# (Optional) Configure and save machine/cluster preferences.\n# This only has to be done once and will persist across sessions.\ncluster = mr.Cluster()\ncluster.set(results_dir=\"/path/to/save/results\", data_dir=\"/path/to/datasets\")\ncluster.save()\n# OR set these as environment variables.\nos.environ[\"MEDDLR_RESULTS_DIR\"] = \"/path/to/save/results\"\nos.environ[\"MEDDLR_DATASETS_DIR\"] = \"/path/to/datasets\"\n```\n\nDetailed instructions are available in [Getting Started](GETTING_STARTED.md).\n\n## Visualizations\nUse [MeddlrViz](https://github.com/ad12/meddlr-viz) to visualize your medical imaging datasets, ML models, and more!\n\n```bash\npip install meddlr-viz\n```\n\n\u003cdiv align=\"center\"\u003e\n\n\u003cimage src=\"https://github.com/ad12/meddlr-viz/blob/main/static/brats.gif\" height=400 alt=\"A gallery of images from the BRATS dataset\" /\u003e\n\u003c/div\u003e\n\n## 🐘 Model Zoo\nEasily 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).\n\nTo use them, pass the URLs for the config and weights (model) files to `mr.get_model_from_zoo`:\n\n```python\nimport meddlr as mr\n\nmodel = mr.get_model_from_zoo(\n  cfg_or_file=\"https://huggingface.co/arjundd/vortex-release/resolve/main/mridata_knee_3dfse/Supervised/config.yaml\",\n  weights_path=\"https://huggingface.co/arjundd/vortex-release/resolve/main/mridata_knee_3dfse/Supervised/model.ckpt\",\n)\n```\n\n## 📓 Projects\nCheck out some [projects](projects) built with meddlr!\n\n## ✏️ Contributing\nWant 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.\n\n## Acknowledgements\nMeddlr's design for rapid experimentation and benchmarking is inspired by [detectron2](https://github.com/facebookresearch/detectron2).\n\n## About\nIf you use Meddlr for your work, please consider citing the following work:\n\n```\n@article{desai2021noise2recon,\n  title={Noise2Recon: A Semi-Supervised Framework for Joint MRI Reconstruction and Denoising},\n  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},\n  journal={arXiv preprint arXiv:2110.00075},\n  year={2021}\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fad12%2Fmeddlr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fad12%2Fmeddlr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fad12%2Fmeddlr/lists"}