Metadata-Version: 2.1
Name: foundation-cancer-image-biomarker
Version: 1.0.1a5
Summary: Official repo for Foundation Models for Quantitative Biomarker Discovery in Cancer Imaging [INSERT DOI]
Home-page: https://aim.hms.harvard.edu/foundation-cancer-image-biomarker
License: MIT
Author: Suraj Pai
Author-email: bspai@bwh.harvard.edu
Requires-Python: >=3.9,<3.12
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Dist: absl-py (==2.1.0)
Requires-Dist: aenum (==3.1.15)
Requires-Dist: aiohappyeyeballs (==2.4.3)
Requires-Dist: aiohttp (==3.10.10)
Requires-Dist: aiosignal (==1.3.1)
Requires-Dist: antlr4-python3-runtime (==4.9.3)
Requires-Dist: appdirs (==1.4.4)
Requires-Dist: asttokens (==2.4.1)
Requires-Dist: async-timeout (==4.0.3)
Requires-Dist: attrs (==24.2.0)
Requires-Dist: babel (==2.16.0)
Requires-Dist: cachetools (==5.5.0)
Requires-Dist: certifi (==2024.8.30)
Requires-Dist: charset-normalizer (==3.4.0)
Requires-Dist: cleo (==2.1.0)
Requires-Dist: click (==8.1.7)
Requires-Dist: colorama (==0.4.6)
Requires-Dist: comm (==0.2.2)
Requires-Dist: contourpy (==1.3.0)
Requires-Dist: crashtest (==0.4.1)
Requires-Dist: cycler (==0.12.1)
Requires-Dist: dataclasses (==0.6)
Requires-Dist: dcmrtstruct2nii (==5)
Requires-Dist: decorator (==5.1.1)
Requires-Dist: distlib (==0.3.9)
Requires-Dist: docker-pycreds (==0.4.0)
Requires-Dist: exceptiongroup (==1.2.2)
Requires-Dist: executing (==2.1.0)
Requires-Dist: filelock (==3.16.1)
Requires-Dist: fire (==0.5.0)
Requires-Dist: fonttools (==4.54.1)
Requires-Dist: frozenlist (==1.5.0)
Requires-Dist: fsspec (==2024.10.0)
Requires-Dist: ghp-import (==2.1.0)
Requires-Dist: gitdb (==4.0.11)
Requires-Dist: gitpython (==3.1.43)
Requires-Dist: google-api-core (==2.23.0)
Requires-Dist: google-auth (==2.36.0)
Requires-Dist: google-cloud-core (==2.4.1)
Requires-Dist: google-cloud-storage (==2.18.2)
Requires-Dist: google-crc32c (==1.6.0)
Requires-Dist: google-resumable-media (==2.7.2)
Requires-Dist: googleapis-common-protos (==1.66.0)
Requires-Dist: grpcio (==1.67.1)
Requires-Dist: hydra-core (==1.3.2)
Requires-Dist: idna (==3.10)
Requires-Dist: imageio (==2.36.0)
Requires-Dist: importlib-metadata (==8.5.0)
Requires-Dist: importlib-resources (==6.4.5)
Requires-Dist: ipython (==8.18.1)
Requires-Dist: ipywidgets (==8.1.5)
Requires-Dist: itk (==5.4.0)
Requires-Dist: itk-core (==5.4.0)
Requires-Dist: itk-filtering (==5.4.0)
Requires-Dist: itk-io (==5.4.0)
Requires-Dist: itk-numerics (==5.4.0)
Requires-Dist: itk-registration (==5.4.0)
Requires-Dist: itk-segmentation (==5.4.0)
Requires-Dist: jedi (==0.19.2)
Requires-Dist: jinja2 (==3.1.4)
Requires-Dist: joblib (==1.4.2)
Requires-Dist: jsonschema (==3.2.0)
Requires-Dist: jupyterlab-widgets (==3.0.13)
Requires-Dist: kiwisolver (==1.4.7)
Requires-Dist: lazy-loader (==0.4)
Requires-Dist: lightly (==1.4.19)
Requires-Dist: lightly-utils (==0.0.2)
Requires-Dist: lightning-utilities (==0.11.8)
Requires-Dist: loguru (==0.6.0)
Requires-Dist: markdown (==3.7)
Requires-Dist: markupsafe (==3.0.2)
Requires-Dist: matplotlib (==3.9.2)
Requires-Dist: matplotlib-inline (==0.1.7)
Requires-Dist: mergedeep (==1.3.4)
Requires-Dist: mkdocs (==1.6.1)
Requires-Dist: mkdocs-get-deps (==0.2.0)
Requires-Dist: mkdocs-material (==9.5.44)
Requires-Dist: mkdocs-material-extensions (==1.3.1)
Requires-Dist: monai (==1.4.0)
Requires-Dist: mpmath (==1.3.0)
Requires-Dist: multidict (==6.1.0)
Requires-Dist: networkx (==3.2.1)
Requires-Dist: nibabel (==5.3.2)
Requires-Dist: numpy (==1.26.4)
Requires-Dist: nvidia-cublas-cu12 (==12.4.5.8)
Requires-Dist: nvidia-cuda-cupti-cu12 (==12.4.127)
Requires-Dist: nvidia-cuda-nvrtc-cu12 (==12.4.127)
Requires-Dist: nvidia-cuda-runtime-cu12 (==12.4.127)
Requires-Dist: nvidia-cudnn-cu12 (==9.1.0.70)
Requires-Dist: nvidia-cufft-cu12 (==11.2.1.3)
Requires-Dist: nvidia-curand-cu12 (==10.3.5.147)
Requires-Dist: nvidia-cusolver-cu12 (==11.6.1.9)
Requires-Dist: nvidia-cusparse-cu12 (==12.3.1.170)
Requires-Dist: nvidia-nccl-cu12 (==2.21.5)
Requires-Dist: nvidia-nvjitlink-cu12 (==12.4.127)
Requires-Dist: nvidia-nvtx-cu12 (==12.4.127)
Requires-Dist: omegaconf (==2.3.0)
Requires-Dist: opencv-python (==4.10.0.84)
Requires-Dist: packaging (==24.2)
Requires-Dist: paginate (==0.5.7)
Requires-Dist: pandas (==1.5.3)
Requires-Dist: parso (==0.8.4)
Requires-Dist: pathspec (==0.12.1)
Requires-Dist: pexpect (==4.9.0)
Requires-Dist: pillow (==11.0.0)
Requires-Dist: pip (==24.3.1)
Requires-Dist: platformdirs (==4.3.6)
Requires-Dist: platipy (==0.4.1)
Requires-Dist: project-lighter (==0.0.2a19)
Requires-Dist: prompt-toolkit (==3.0.48)
Requires-Dist: propcache (==0.2.0)
Requires-Dist: proto-plus (==1.25.0)
Requires-Dist: protobuf (==4.25.5)
Requires-Dist: psutil (==6.1.0)
Requires-Dist: ptyprocess (==0.7.0)
Requires-Dist: pure-eval (==0.2.3)
Requires-Dist: pyasn1 (==0.6.1)
Requires-Dist: pyasn1-modules (==0.4.1)
Requires-Dist: pydantic (==1.10.13)
Requires-Dist: pydicom (==2.4.4)
Requires-Dist: pydicom-seg (==0.4.1)
Requires-Dist: pygments (==2.18.0)
Requires-Dist: pymdown-extensions (==10.12)
Requires-Dist: pymedphys (==0.40.0)
Requires-Dist: pynetdicom (==2.0.2)
Requires-Dist: pynrrd (==1.1.1)
Requires-Dist: pyparsing (==3.2.0)
Requires-Dist: pyrsistent (==0.20.0)
Requires-Dist: python-dateutil (==2.9.0.post0)
Requires-Dist: pytorch-lightning (==2.4.0)
Requires-Dist: pytz (==2024.2)
Requires-Dist: pyyaml (==6.0.2)
Requires-Dist: pyyaml-env-tag (==0.1)
Requires-Dist: rapidfuzz (==3.10.1)
Requires-Dist: regex (==2024.11.6)
Requires-Dist: requests (==2.32.3)
Requires-Dist: rsa (==4.9)
Requires-Dist: rt-utils (==1.2.7)
Requires-Dist: scikit-image (==0.24.0)
Requires-Dist: scikit-learn (==1.5.2)
Requires-Dist: scipy (==1.10.0)
Requires-Dist: seaborn (==0.13.2)
Requires-Dist: sentry-sdk (==2.18.0)
Requires-Dist: setproctitle (==1.3.3)
Requires-Dist: setuptools (==75.4.0)
Requires-Dist: simpleitk (==2.4.0)
Requires-Dist: six (==1.16.0)
Requires-Dist: smmap (==5.0.1)
Requires-Dist: stack-data (==0.6.3)
Requires-Dist: sympy (==1.13.1)
Requires-Dist: tensorboard (==2.18.0)
Requires-Dist: tensorboard-data-server (==0.7.2)
Requires-Dist: termcolor (==2.5.0)
Requires-Dist: thedicomsort (==1.0.1)
Requires-Dist: threadpoolctl (==3.5.0)
Requires-Dist: tifffile (==2024.8.30)
Requires-Dist: tomlkit (==0.13.2)
Requires-Dist: torch (==2.5.1)
Requires-Dist: torchmetrics (==1.6.0)
Requires-Dist: torchvision (==0.20.1)
Requires-Dist: tornado (==6.4.1)
Requires-Dist: tqdm (==4.67.0)
Requires-Dist: traitlets (==5.14.3)
Requires-Dist: triton (==3.1.0)
Requires-Dist: typing-extensions (==4.12.2)
Requires-Dist: urllib3 (==2.2.3)
Requires-Dist: virtualenv (==20.27.1)
Requires-Dist: vtk (==9.3.1)
Requires-Dist: wandb (==0.16.6)
Requires-Dist: watchdog (==6.0.0)
Requires-Dist: wcwidth (==0.2.13)
Requires-Dist: werkzeug (==3.1.3)
Requires-Dist: wget (==3.2)
Requires-Dist: widgetsnbextension (==4.0.13)
Requires-Dist: yarl (==1.17.1)
Requires-Dist: zipp (==3.21.0)
Project-URL: Repository, https://github.com/AIM-Harvard/foundation-cancer-image-biomarker
Description-Content-Type: text/markdown


<div align="center">
This is the official repository for the paper
<br/><br/>
</div>

<div style="display: flex; flex-direction: column; align-items: center;">
    <img src="./docs/assets/Header.png" style="width: 100%;"/>
    <div style="display: flex; justify-content: space-between; width: 100%;">
        <img src="./docs/assets/Mhub_image.png" style="width: 49%;"/>
        <img src="./docs/assets/Mhub_image2.png" style="width: 50%;"/>
    </div>
    <a href="https://www.nature.com/articles/s42256-024-00807-9"><img src="./docs/assets/readpaper_logo.png" style="width: 100%;"></a>
</div>

<br/><br/>
<div align="center">

[![Build Status](https://github.com/AIM-Harvard/foundation-cancer-image-biomarker/actions/workflows/build.yml/badge.svg)](https://github.com/AIM-Harvard/foundation-cancer-image-biomarker/actions/workflows/build.yml)
[![Python Version](https://img.shields.io/pypi/pyversions/foundation-cancer-image-biomarker.svg)](https://pypi.org/project/foundation-cancer-image-biomarker/)
[![Dependencies Status](https://img.shields.io/badge/dependencies-up%20to%20date-brightgreen.svg)](https://github.com/AIM-Harvard/foundation-cancer-image-biomarker/pulls?utf8=%E2%9C%93&q=is%3Apr%20author%3Aapp%2Fdependabot)
[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
[![Security: bandit](https://img.shields.io/badge/security-bandit-green.svg)](https://github.com/PyCQA/bandit)
[![Pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/AIM-Harvard/foundation-cancer-image-biomarker/blob/master/.pre-commit-config.yaml)
[![Semantic Versions](https://img.shields.io/badge/%20%20%F0%9F%93%A6%F0%9F%9A%80-semantic--versions-e10079.svg)](https://github.com/AIM-Harvard/foundation-cancer-image-biomarker/releases)
[![License](https://img.shields.io/github/license/AIM-Harvard/foundation-cancer-image-biomarker)](https://github.com/AIM-Harvard/foundation-cancer-image-biomarker/blob/master/LICENSE)
[![Coverage](docs/assets/images/coverage.svg)](https://github.com/AIM-Harvard/foundation-cancer-image-biomarker/blob/master/docs/assets/images/coverage.svg)



---
**NOTE:**
 For detailed documentation check our [website](https://aim-harvard.github.io/foundation-cancer-image-biomarker/) 

---

</div>

