{"id":37702280,"url":"https://github.com/masilab/deeplungscreening","last_synced_at":"2026-01-16T13:01:16.504Z","repository":{"id":129622896,"uuid":"318541330","full_name":"MASILab/DeepLungScreening","owner":"MASILab","description":null,"archived":false,"fork":false,"pushed_at":"2025-04-29T20:58:31.000Z","size":66863,"stargazers_count":4,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-04-29T21:34:23.837Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/MASILab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2020-12-04T14:30:04.000Z","updated_at":"2025-04-16T02:38:48.000Z","dependencies_parsed_at":null,"dependency_job_id":"ef3402f7-4982-4661-98aa-87deeed58595","html_url":"https://github.com/MASILab/DeepLungScreening","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/MASILab/DeepLungScreening","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MASILab%2FDeepLungScreening","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MASILab%2FDeepLungScreening/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MASILab%2FDeepLungScreening/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MASILab%2FDeepLungScreening/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MASILab","download_url":"https://codeload.github.com/MASILab/DeepLungScreening/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MASILab%2FDeepLungScreening/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28478886,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T11:59:17.896Z","status":"ssl_error","status_checked_at":"2026-01-16T11:55:55.838Z","response_time":107,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2026-01-16T13:01:15.914Z","updated_at":"2026-01-16T13:01:16.497Z","avatar_url":"https://github.com/MASILab.png","language":"Python","readme":"# DeepLungScreening Overview\n\nThis is the Deep Learning Open-source Lung cancer risk estimation repository, with PyTorch implementations. We prevoide source code, running tutorial, pre-trained model, docker, and [example image](https://drive.google.com/drive/folders/1gyKfWa_vmI_0K0dZ_lBUynCnOJhy3dKU?usp=sharing) in this repository.\n\nPlease see the requirement in the Dockerfile. Different version packages should be easy to adapt (not guarantee). \n\n# Tutorial\n\nAll the steps can be find in run_all.sh. A INPUTS and OUTPUTS example can be found here. \n\n\n\u003cimg src=\"./Figure/prep_detect_extract.png\" alt=\"drawing\" class=\"center\" width=\"600\"/\u003e\n\u003cp align=\"center\"\u003e Fig. 1. Step 1-3 are summarized in this Figure \u003c/p\u003e\n\n\n## step 1: image pre-process\n\n\u003e python3 ./1_preprocess/step1_main.py --sess_csv ${SPLIT_CSV} --prep_root ${PREP_ROOT} --ori_root ${ORI_ROOT} \n\n```${SPLIT_CSV}``` is the csv file stores the scan list (and meta data) you want to test. \n```${PREP_ROOT}``` is the data folder saves the pre-processed result.\n```${ORI_ROOT}``` is the data folder stores the scans you want to test.\n\n## step 2: nodule detection\n\n\u003e python3 ./2_nodule_detection/step2_main.py --sess_csv ${SPLIT_CSV} --bbox_root ${BBOX_ROOT} --prep_root ${PREP_ROOT} \n\n```${BBOX_ROOT}``` is the data folder stores the nodule detection results.\n\n\n## step 3: feature extraction\n\n\u003e python3 ./3_feature_extraction/step3_main.py --sess_csv ${SPLIT_CSV} --bbox_root ${BBOX_ROOT} --prep_root ${PREP_ROOT} --feat_root ${FEAT_ROOT}\n\n```${FEAT_ROOT}``` is the data folder stores the image feature results.\n\n\u003cimg src=\"./Figure/co_learning.png\" alt=\"drawing\" class=\"center\" width=\"600\"/\u003e\n\u003cp align=\"center\"\u003e Fig. 2. Step 4 are summarized in this Figure\u003c/p\u003e\n\n## step 4: co-learning of meta data and image\n\n\u003e python3 ./4_co_learning/step4_main.py --sess_csv ${SPLIT_CSV} --feat_root ${FEAT_ROOT} --save_csv_path ${PRED_CSV}\n\n```${PRED_CSV}``` is the predicted result from deep learning method.\n\n# Docker\n\nThe Dockerfile is shared in this repository. The docker image rg15/deeplung:0.3 can be downloaded from DockHub. \n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmasilab%2Fdeeplungscreening","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmasilab%2Fdeeplungscreening","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmasilab%2Fdeeplungscreening/lists"}