This is the codebase for MOSAICFlow (MultimOdal Spatial Alignment and Integration with Conditional Flow matching), a computational method to perform physical and morphological alignment on spatial data with multimple modalities.
There are two main functions:
src/MOSAICFlow/physical/physical_align: Given a pair of spatial slices, potentially from different modalities, performs physical alignment to affine register one slice onto the other, and compute a probabilistic mappingsrc/MOSAICFlow/morphological/morphological_align: Give a pair of physically aligned slices and the probabilistic mapping, performs morphological alignment to learn a neural ODE between the two slices
This is a very preliminary version of the codebase to get you started on using our tool. We are actively working on the project and will include more functionalities soon.
If you encounter any problem running the software, please contact Xinhao Liu at xl5434@princeton.edu or Hongyu Zheng at hz7140@princeton.edu.