Welcome to 3d_OT's documentation!
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.. toctree::
   :maxdepth: 2
   :caption: Contents:

   Installation
   Single_Omics_spatial_domain_identification/index
   Multi_Omics_spatial_domain_identification/index
   Single_Omics_alignment/index
   Mouse_brain_p22_alignment/index
   3Dreconstruction
   cross_platform



.. image:: _static/3d_OT.png
   :alt: 3d-OT Logo
   :width: 1000px
   :height: 400px
   :align: center   


Overview
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**3d-OT leverages the PointNet++ model and optimal transport with soft communication as its foundation.**  Through a modular integration approach, it seamlessly supports single-modal, multi-modal, and diverse spatial omics data from various technologies.  
By precisely extracting meaningful features from positional information, 3d-OT achieves high-resolution analysis of spatial omics data.  Utilizing the framework of **soft communication optimal transport**, it effectively tackles challenges such as 
**non-rigid alignment** and **inconsistent resolution** during the alignment process.  
Furthermore, it introduces a novel evaluation metric, the **Chamfer distance**, to assess alignment quality.