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https://github.com/cns-iu/hra-3d-cell-generation-api
API to generate 3D Cells inside Anatomical Structures
https://github.com/cns-iu/hra-3d-cell-generation-api
human-reference-atlas
Last synced: about 1 month ago
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API to generate 3D Cells inside Anatomical Structures
- Host: GitHub
- URL: https://github.com/cns-iu/hra-3d-cell-generation-api
- Owner: cns-iu
- Created: 2024-03-19T18:47:05.000Z (10 months ago)
- Default Branch: main
- Last Pushed: 2024-08-22T16:15:36.000Z (5 months ago)
- Last Synced: 2024-08-23T18:21:49.169Z (5 months ago)
- Topics: human-reference-atlas
- Language: C++
- Homepage:
- Size: 406 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# 3d-cell-generation-api
**Version:** 1.0.0
**Release date:** 15 June 2024
## Overview:
As the core algorithms for the paper *Constructing and Using Cell Type Populations for the Human Reference Atlas*, generating 3D cells inside anatomical structures includes two steps: estimating the number of cells in anatomical structures and generating the location of the cells inside the anatomical structures. We design an algorithm for the cell type estimation based on the experimental datasets by using the collision detection API https://github.com/hubmapconsortium/hra-tissue-block-annotation as well as a 3D cell generation algorithm using the Computational Geometry Algorithm Library (CGAL). This project provides
1. the proposed algorithm for randomly generate 3D cell locations inside any mesh of anatomical structures using CGAL.
2. an Node.js API using Express to generate 3D cells given the distribution of the cells and the mesh of the anatomical structure.
## Installation Instructions
1. CMake
```bash
sudo apt-get cmake
```
2. Boost
```bash
sudo apt-get update
sudo apt-get install libboost-all-dev
```
3. GMP
```bash
sudo apt-get install libgmp-dev
```
4. MPFR
```bash
sudo apt-get install libmpfr-dev
```
5. CGAL
```bash
sudo apt-get install libcgal-dev
```
6. Eigen3
```bash
sudo apt install libeigen3-dev
```
7. Node Dependencies
```bash
npm ci
```
## Compilation
We use CMake to configure the program with third-party dependencies and generate the native build system by creating a CMakeLists.txt file.
1. for C++ server:
```bash
cd $server
mkdir build
cd build
cmake ..
make
```
Then, copy the binary executable to the main directory
```bash
cp generate_cell_ctpop ../../
```
## Usage
1. Start Node.js API:
```bash
npm start
```
## Example
POST http://server_ip:port/mesh-3d-cell-population
- JSON [request example](examples/test-request.json):
```json
{
"file": "https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-female-left/v1.3/assets/3d-vh-f-kidney-l.glb",
"file_subpath": "VH_F_renal_pyramid_L_a",
"num_nodes": 10,
"node_distribution": {
"KEY1": 0.1,
"KEY2": 0.3
}
}
```
- Request as a CURL command:
```bash
curl -d '@examples/test-request.json' -H "Content-Type: application/json" -X POST http://localhost:8080/mesh-3d-cell-population
```
- CSV/text response example:
```text
x,y,z,Cell Type
0.0579039,0.269139,-0.103702,KEY1
0.0532916,0.258096,-0.104511,KEY2
0.0520264,0.279228,-0.110894,KEY2
0.0568783,0.264194,-0.10985,KEY2
```
## Docker
A docker container for the API can be built locally:
```bash
docker build . -t hra-3d-cell-generation-api
```
And run locally:
```bash
docker run -p8080:8080 -it hra-3d-cell-generation-api
```
## Deployed version
The deployed version of this API is at https://apfvtab7fp.us-east-2.awsapprunner.com/mesh-3d-cell-population . You can use the same CURL command to test:
```bash
curl -d '@examples/test-request.json' -H "Content-Type: application/json" -X POST https://apfvtab7fp.us-east-2.awsapprunner.com/mesh-3d-cell-population
```