https://github.com/dhchenx/medsim3d

Medical Simulation Framework in the 3D Environment
https://github.com/dhchenx/medsim3d

3d-modeling human-body-reconstruction medical-education simulation visible-human-project

Last synced: 21 days ago
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Medical Simulation Framework in the 3D Environment

• Host: GitHub
• URL: https://github.com/dhchenx/medsim3d
• Owner: dhchenx
• Created: 2022-07-30T18:20:04.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2022-09-02T05:34:09.000Z (over 2 years ago)
• Last Synced: 2024-11-08T18:05:09.867Z (about 1 month ago)
• Topics: 3d-modeling, human-body-reconstruction, medical-education, simulation, visible-human-project
• Language: Python
• Homepage: https://pypi.org/project/MedSim3D/
• Size: 39.4 MB
• Stars: 0
• Watchers: 1
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
## 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](https://www.nlm.nih.gov/databases/download/vhp.html). 

```python

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

```python

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

```python

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

![MedSim3D image processing](https://dhchenx.github.io/projects/MedSim3D/medsim3d-image-processing.png)

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

![MedSim3D agent-based 3D modeing](https://dhchenx.github.io/projects/MedSim3D/medsim3d-agent-based-modeling.png)

### Credits

- [The NLM Visible Human Project](https://www.nlm.nih.gov/research/visible/visible_human.html)

- [Open3D](http://www.open3d.org/)

### License

The `MedSim3D` toolkit is provided by [Donghua Chen](https://github.com/dhchenx) with MIT License.