3D Corridor for Tissue Block Re-registration

Version:: 1.0.0

Release date: 9 Feb 2024

Overview:

A C++ library for http service for 3D corridor generation given a RUI Registration.

Dependencies:

For C++ libraries:

1. Download CGAL 5.5.3 Extract the compressed file to the 'corridor_http_service' folder.

2. CMake

   sudo apt-get install build-essential libssl-dev
   cd /tmp
   wget https://github.com/Kitware/CMake/releases/download/v3.20.0/cmake-3.20.0.tar.gz
   tar -zxvf cmake-3.20.0.tar.gz
   cd cmake-3.20.0
   ./bootstrap
   make
   sudo make install

3. Boost

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

4. GMP

   sudo apt-get install libgmp-dev

5. MPFR

   sudo apt-get install libmpfr-dev

6. Eigen3

   sudo apt install libeigen3-dev

7. assimp

   sudo apt-get install libassimp-dev

8. cpprestsdk

   sudo apt-get install libcpprest-dev

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 collision detection and volume computation:

   cd $src
   mkdir build
   cd build
   cmake ..
   make

Model

1. AS: meshes that anatomical structure as the basic unit, e.g., renal pyramid is an anatomical structure and there is a renal_pyramid.off which is the mesh of renal pyramid in off format.
2. AS_filling_hole: AS after hole filling
3. plain_with_holes: fine-grained meshes that leaf node in glb file as the basic unit, e.g., VH_F_renal_papilla_L_g.off is a basic unit.
4. plain_filling_hole: plain_with_hole after hole filling
5. ASCT-B_3D_Models_Mapping.csv: famous ASCT-B table
6. organ_origins_meter.csv: origin coordinates of organs generated by extract_origins.py in scripts folder.

Usage

Server side:

1. start http service and receive json request:

   cd $corridor_http_service/build
   ./server2 path_of_3d_model_origins.csv path_of_asct_b.csv body_path path_of_reference_organ_data server_ip port 
   e.g., ./server2 /model/organ_origins_meter_v1.4.csv /model/asct-b-3d-models-crosswalk.csv /model/plain_manifold_filling_hole_v1.4/ /model/reference-organ-data.json 10.0.2.15 12345
   

   note: 3d_model_origins.csv, asct_b.csv, examples of body_path , and reference-organ-data.json are provided in model folder.

Client side:

POST http://server_ip:port/get-corridor

• JSON request example

{
  "@id": "http://purl.org/ccf/1.5/f31c1726-c693-4734-8c1c-4f1d64bbe034",
  "@type": "SpatialEntity",
  "ccf_annotations": [
      "http://purl.obolibrary.org/obo/UBERON_0002015",
      "http://purl.obolibrary.org/obo/UBERON_0001225",
      "http://purl.obolibrary.org/obo/UBERON_0002189",
      "http://purl.obolibrary.org/obo/UBERON_0000362",
      "http://purl.obolibrary.org/obo/UBERON_0001228",
      "http://purl.obolibrary.org/obo/UBERON_0004200",
      "http://purl.obolibrary.org/obo/UBERON_0001284",
      "http://purl.obolibrary.org/obo/UBERON_0006517",
      "http://purl.obolibrary.org/obo/UBERON_0001227",
      "http://purl.obolibrary.org/obo/UBERON_0008716"
  ],
  "creation_date": "2021-10-03",
  "creator": "Amanda Knoten",
  "creator_first_name": "Amanda",
  "creator_last_name": "Knoten",
  "dimension_units": "millimeter",
  "placement": {
      "@id": "http://purl.org/ccf/1.5/f31c1726-c693-4734-8c1c-4f1d64bbe034_placement",
      "@type": "SpatialPlacement",
      "placement_date": "2021-10-03",
      "rotation_order": "XYZ",
      "rotation_units": "degree",
      "scaling_units": "ratio",
      "target": "http://purl.org/ccf/latest/ccf.owl#VHMLeftKidney",
      "translation_units": "millimeter",
      "x_rotation": 105,
      "x_scaling": 1,
      "x_translation": 50.009,
      "y_rotation": 131,
      "y_scaling": 1,
      "y_translation": 65.904,
      "z_rotation": 44,
      "z_scaling": 1,
      "z_translation": 60.555
  },
  "x_dimension": 5,
  "y_dimension": 6,
  "z_dimension": 2
}

• Request as a CURL command on staging server:

curl -d '@examples/test-corridor.json' -H "Content-Type: application/json" -X POST https://dwwcpwad72.us-east-2.awsapprunner.com/get-corridor -o output_corridor.glb

Input: RUI Registration Produces: result GLB file