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

the proposed algorithm for randomly generate 3D cell locations inside any mesh of anatomical structures using CGAL.
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

CMake
```
sudo apt-get cmake
```

Boost

sudo apt-get update
sudo apt-get install libboost-all-dev

GMP
```
sudo apt-get install libgmp-dev
```
MPFR
```
sudo apt-get install libmpfr-dev
```
CGAL
```
sudo apt-get install libcgal-dev
```
Eigen3
```
sudo apt install libeigen3-dev
```
Node Dependencies
```
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.

for C++ server:

cd $server
mkdir build
cd build
cmake ..
make

Then, copy the binary executable to the main directory

cp generate_cell_ctpop ../../

Usage

Start Node.js API:
```
npm start
```

Example

POST http://server_ip:port/mesh-3d-cell-population

JSON request example:

{
"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:

curl -d '@examples/test-request.json' -H "Content-Type: application/json" -X POST http://localhost:8080/mesh-3d-cell-population

CSV/text response example:

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:

docker build . -t hra-3d-cell-generation-api

And run locally:

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:

curl -d '@examples/test-request.json' -H "Content-Type: application/json" -X POST https://apfvtab7fp.us-east-2.awsapprunner.com/mesh-3d-cell-population

cns-iu / hra-3d-cell-generation-api

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