hra-amap

HRA-AMAP

HRA-AMAP (Human Reference Atlas – Automated Mapping and Projection) enables automated projection of tissue blocks from a source organ to a new reference organ—typically aligned with the Human Reference Atlas (HRA)—as part of the HuBMAP initiative.

🚀 User Setup Instructions

1. Clone and install the repository directly from GitHub:

   pip install git+https://github.com/cns-iu/hra-amap.git@main
   

2. Make sure you have a working C++ build environment (e.g., g++, make) available on your system.

3. Install BCPD (an essential component of this project)

   Please follow the BCPD Installation Instructions if it is not already set up on your machine.

4. You are now ready to run the millitome registration commands (stage-1, stage-2, or run). See Usage Instructions for details below.

🧑‍💻 Developer Setup Instructions

To contribute or develop this project locally, follow the steps below:

1. Clone the repository:

   git clone https://github.com/cns-iu/hra-amap.git
   cd hra-amap
   

2. Install BCPD by following BCPD Installation Instructions.
3. Install [Node.js] (https://nodejs.org/en/download/) and run the command (required create RUI JSONs for Millitomes):

   npx github:hubmapconsortium/hra-rui-locations-processor help
   

4. Install Hatch (used to build and install hra-amap package locally):

   pip install hatch
   

5. Install dependencies for development:

   pip install -e .
   

6. Build the package (compiles the BCPD binary and packages everything)

   hatch build
   

7. Install the built wheel (adjust version if needed)

   pip install dist/hra_amap-0.5.0-py3-none-any.whl
   

8. (Optional) Uninstall to reset or clean up

   pip uninstall hra-amap
   

9. You are now ready to run the millitome registration commands (stage-1, stage-2, or run). See Usage Instructions for details below.

🧬 Adding a New Millitome Dataset

To register a new millitome organ, organize the necessary configuration and input files as described below.

📁 Directory Structure

Each millitome dataset should be placed in its own subdirectory under:

input-data/millitome/<organ-name>-<sex>-<source>/<version>/

📦 Required Files

Place the following files inside the directory: | Filename | Description | |-----------------------|------------------------------------------------------------------| | `config.yaml` | Configuration file with metadata and registration parameters. | | `source.glb` | The `.glb` version of the source mesh for visualization in RUI. | | `target.glb` | The `.glb` version of the target mesh for visualization in RUI. |

⚙️ Millitome Registration Usage Instructions

🔹 Stage 1: Generates the projected 3D model data

It takes a configuration file with RUI locations and donor metadata, and generates projection data that serves as input for Stage 2.

hra-amap-stage-1 \
    --config <path_to_config.yaml> \
    --output_path <path_to_output_directory>

🔹 Stage 2: Produces the final registered organ model

It takes the output from Stage 1 (a projection file), a configuration file, and produces the final registered organ models.

hra-amap-stage-2 \
    --stage1_projection_path <path_to_projections.pickle.gz> \
    --output_path <path_to_output_directory> \
    --config <path_to_config.yaml>

🔹 Run All: Register All Available Millitome Organs This command automates both Stage 1 and Stage 2 for all available millitome configurations found in the input-data/millitome/ directory.

hra-amap-run

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