HRA-AMap - Bidirectional Projections Between Human Atlas Systems for Data and Code Interoperability

Code for AMap project.

This repository aims to enable projection of tissue blocks registrered to a source organ to a new reference organ (usually the Human Reference Atlas, part of HuBMAP).

Setup instructions:

1. Clone the repository with git clone https://github.com/cns-iu/hra-amap.git

2. Clone the repository git clone https://github.com/ohirose/bcpd.git that implements the Bayesian Coherent Point Drift algorithm based on the following paper A Bayesian Formulation of Coherent Point Drift. The repository is ~1GB in file size hence it is not shipped with our repository and requires additional setup:

   • For Windows

     1. No setup required.

   • For MacOS and Linux

     1. Install the OpenMP and the LAPACK libraries if not installed. For MacOS, make sure XCode is installed.

     2. Type make OPT=-DUSE_OPENMP ENV=<your-environment>. Substitute <uyour-environment> with LINUX for Linux, HOMEBREW_INTEL for Intel Macs and HOMEBREW for Macs with Apple Silicon.

3. Ensure that the two repositories (hra-amap and bcpd) are at the same root level.

4. To run a quick registration using the provided pipeline, please see notebooks/pipeline_usage