MedSim3D: Medical Simulation Framework in the 3D environment

The MedSim3D framework provides a general programmable platform for 3D modeling and simulation in medical education.

Installation

    pip install MedSim3D

Dependencies

tqdm, requests, numpy, cv2, shapely, quick-csv, pillow, pandas, pyntcloud, sklearn, matplotlib, scipy, skimage

Examples

Example 1: Download datasets from the Visible Human Project.

from medsim3d.vhp.downloader import VHPDownloader
vhp_downloader=VHPDownloader()
vhp_downloader.download_datasets(
    gender="Male", # Male or Female
    body_part="head", 
    # Options: abdomen, head, legs, pelvis, thighs, thorax
    save_folder="datasets/male/head")

Example 2: Build human body part 3D models from colored slices

from medsim3d.vhp.pipeline_bodypart import  *
# A pipeline to build body parts in a simple way
pipeline_pelvis=PipelineBodyPart(
    gender="Female",
    body_part="pelvis", 
    # Options: abdomen, head, legs, pelvis, thighs, thorax
    root_folder='../datasets/Female'
)
pipeline_pelvis.run(force_download=True)

Example 3: Build human full-body 3D models from CT images

from medsim3d.vhp.pipeline_human import *
pipeline_human=PipelineHuman(
    gender='Male',
    ct_type='frozenCT', # normalCT
    root_path='../datasets/Male'
)
pipeline_human.run(force_download=True)

Screenshots

(1) Medical image processing using the VHP data sets

(2) 3D agent-based modeling in NetLogo using VHP data sets

Credits

• The NLM Visible Human Project
• Open3D

License

The MedSim3D toolkit is provided by Donghua Chen with MIT License.