{"id":19480325,"url":"https://github.com/hasibzunair/uniformizing-3d","last_synced_at":"2025-04-25T15:31:33.210Z","repository":{"id":60099588,"uuid":"200432563","full_name":"hasibzunair/uniformizing-3D","owner":"hasibzunair","description":"[MICCAI'2020 PRIME] Uniformizing Techniques to Process CT scans with 3D CNNs for Tuberculosis Severity Estimation.","archived":false,"fork":false,"pushed_at":"2022-08-11T16:40:59.000Z","size":24781,"stargazers_count":60,"open_issues_count":0,"forks_count":7,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-04-03T23:41:15.357Z","etag":null,"topics":["3d-data","classification","computed-tomography","convolutional-neural-networks","deep-learning","information-retrieval","volumetric-data"],"latest_commit_sha":null,"homepage":"","language":"Jupyter 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Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Intro\n\nThis is official code of MICCAI'2020 PRIME workshop paper: \u003cbr\u003e\n*Uniformizing Techniques to Process CT scans with 3D CNNs for Tuberculosis Prediction* ([Paper](https://link.springer.com/chapter/10.1007%2F978-3-030-59354-4_15), [arXiv](https://arxiv.org/abs/2007.13224))\n\n### Virtual Presentation at MICCAI'2020 PRIME\n[![IMAGE ALT TEXT HERE](https://img.youtube.com/vi/IP6poudyny4/0.jpg)](https://www.youtube.com/watch?v=IP6poudyny4)\n\n\n### Citation\nIf you use this code or models in your scientific work, please cite the following paper:\n\n```bibtex\n@inproceedings{zunair2020uniformizing,\n  title={Uniformizing Techniques to Process CT Scans with 3D CNNs for Tuberculosis Prediction},\n  author={Zunair, Hasib and Rahman, Aimon and Mohammed, Nabeel and Cohen, Joseph Paul},\n  booktitle={International Workshop on PRedictive Intelligence In MEdicine},\n  pages={156--168},\n  year={2020},\n  organization={Springer}\n}\n```\n\n\n### Data Processing Method\n\nData uniformizing methods\n\n\u003cp align=\"left\"\u003e\n\u003ca href=\"#\"\u003e\u003cimg src=\"asset/algorithm.png\" width=\"100%\"\u003e\u003c/a\u003e\n\u003c/p\u003e\n\n### 3D Convolutional Neural Network\n\n\u003cp align=\"left\"\u003e\n\u003ca href=\"#\"\u003e\u003cimg src=\"asset/network.png\" width=\"100%\"\u003e\u003c/a\u003e\n\u003c/p\u003e\n\n\n\n### Results\n\n\u003cp align=\"left\"\u003e\n\u003ca href=\"#\"\u003e\u003cimg src=\"asset/top_results.png\" width=\"100%\"\u003e\u003c/a\u003e\n\u003c/p\u003e\n\n### Dependencies\n\n*    Ubuntu 14.04\n*    Python 3.6\n*    Tensorflow: 2.0.0\n*    Keras: 2.3.1\n\n### Environment setup\n\nYou can create the appropriate conda environment by running\n\n`conda env create -f environment.yml`\n\n\n### Directory Structure \u0026 Usage\n\nFirst, get the data from [here](https://www.imageclef.org/2019/medical/tuberculosis). Then:\n\n* Run notebooks in order\n* `others`: Contains helper codes to preprocess and visualize samples in dataset.\n\n### Demo\n\nA 🤗 Spaces demo for detecting pneumonia from CT scans using our [method](https://keras.io/examples/vision/3D_image_classification/) is available [here](https://huggingface.co/spaces/keras-io/3D_CNN_Pneumonia). Demo built by [Faizan Shaikh](https://github.com/faizankshaikh).\n\n### This is an extension of previous work\n\nMore details at this [link](https://github.com/hasibzunair/tuberculosis-severity)\n\n```bibtex\nZunair,  H.,  Rahman,  A.,  Mohammed,  N.:   Estimating  Severity  from  CT  Scans\nof  Tuberculosis  Patients  using  3D  Convolutional  Nets  and  Slice  Selection.   In:\nCLEF2019  Working  Notes.  Volume  2380  of  CEUR  Workshop  Proceedings.,\nLugano, Switzerland, CEUR-WS.org\n\u003chttp://ceur-ws.org/Vol-2380\u003e(September 9-12 2019) \n```\nPrevious paper published in CEUR-WS. Paper can be found at [CLEF Working Notes 2019](http://www.dei.unipd.it/~ferro/CLEF-WN-Drafts/CLEF2019/paper_77.pdf) under the section ImageCLEF - Multimedia Retrieval in CLEF.\n\n\n### License\n\nYour driver's license.\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhasibzunair%2Funiformizing-3d","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhasibzunair%2Funiformizing-3d","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhasibzunair%2Funiformizing-3d/lists"}