{"id":22089991,"url":"https://github.com/dhchenx/medsim3d","last_synced_at":"2026-03-17T23:08:51.806Z","repository":{"id":62592761,"uuid":"519590481","full_name":"dhchenx/MedSim3D","owner":"dhchenx","description":"Medical Simulation Framework in the 3D Environment","archived":false,"fork":false,"pushed_at":"2022-09-02T05:34:09.000Z","size":41290,"stargazers_count":2,"open_issues_count":0,"forks_count":2,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-01-01T14:07:34.196Z","etag":null,"topics":["3d-modeling","human-body-reconstruction","medical-education","simulation","visible-human-project"],"latest_commit_sha":null,"homepage":"https://pypi.org/project/MedSim3D/","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/dhchenx.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}},"created_at":"2022-07-30T18:20:04.000Z","updated_at":"2024-12-22T17:48:11.000Z","dependencies_parsed_at":"2022-11-03T23:31:09.723Z","dependency_job_id":null,"html_url":"https://github.com/dhchenx/MedSim3D","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhchenx%2FMedSim3D","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhchenx%2FMedSim3D/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhchenx%2FMedSim3D/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dhchenx%2FMedSim3D/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dhchenx","download_url":"https://codeload.github.com/dhchenx/MedSim3D/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":236139605,"owners_count":19101162,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","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":["3d-modeling","human-body-reconstruction","medical-education","simulation","visible-human-project"],"created_at":"2024-12-01T02:14:52.662Z","updated_at":"2025-10-11T23:30:48.968Z","avatar_url":"https://github.com/dhchenx.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"## MedSim3D: Medical Simulation Framework in the 3D environment\n\nThe `MedSim3D` framework provides a general programmable platform for 3D modeling and simulation in medical education.\n\n### Installation\n\n```\n    pip install MedSim3D\n```\n\n### Dependencies\n\ntqdm, requests, numpy, cv2, shapely, quick-csv, pillow, pandas, pyntcloud, sklearn, matplotlib, scipy, skimage\n\n### Examples\n\nExample 1: Download datasets from [the Visible Human Project](https://www.nlm.nih.gov/databases/download/vhp.html). \n\n```python\nfrom medsim3d.vhp.downloader import VHPDownloader\nvhp_downloader=VHPDownloader()\nvhp_downloader.download_datasets(\n    gender=\"Male\", # Male or Female\n    body_part=\"head\", \n    # Options: abdomen, head, legs, pelvis, thighs, thorax\n    save_folder=\"datasets/male/head\")\n```\n\nExample 2: Build human body part 3D models from colored slices\n\n```python\nfrom medsim3d.vhp.pipeline_bodypart import  *\n# A pipeline to build body parts in a simple way\npipeline_pelvis=PipelineBodyPart(\n    gender=\"Female\",\n    body_part=\"pelvis\", \n    # Options: abdomen, head, legs, pelvis, thighs, thorax\n    root_folder='../datasets/Female'\n)\npipeline_pelvis.run(force_download=True)\n```\n\nExample 3: Build human full-body 3D models from CT images\n\n```python\nfrom medsim3d.vhp.pipeline_human import *\npipeline_human=PipelineHuman(\n    gender='Male',\n    ct_type='frozenCT', # normalCT\n    root_path='../datasets/Male'\n)\npipeline_human.run(force_download=True)\n```\n\n### Screenshots\n\n(1) Medical image processing using the VHP data sets\n\n![MedSim3D image processing](https://dhchenx.github.io/projects/MedSim3D/medsim3d-image-processing.png)\n\n\n(2) 3D agent-based modeling in NetLogo using VHP data sets\n\n![MedSim3D agent-based 3D modeing](https://dhchenx.github.io/projects/MedSim3D/medsim3d-agent-based-modeling.png)\n\n### Credits\n\n- [The NLM Visible Human Project](https://www.nlm.nih.gov/research/visible/visible_human.html)\n- [Open3D](http://www.open3d.org/)\n\n### License\n\nThe `MedSim3D` toolkit is provided by [Donghua Chen](https://github.com/dhchenx) with MIT License.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdhchenx%2Fmedsim3d","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdhchenx%2Fmedsim3d","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdhchenx%2Fmedsim3d/lists"}