PASTE2

PASTE2, the extension of PASTE, is a method for partial alignment and 3D reconstruction of spatial transcriptomics slices when they do not fully overlap in space.

There are three main functions:

1. src/paste2/PASTE2/partial_pairwise_align: Given a pair of ST slices and their overlap percentage, find a partial alignment matrix. Note: In a multi-sample dataset, partial_pairwise_align should be called on each pair of adjacent slices separately.
2. src/paste2/model_selection/select_overlap_fraction: Decide the overlap percentage (s parameter of partial_pairwise_align) between two input ST slices. Note: In a multi-sample dataset, each pair of adjacent slices could have a different overlap percentage, hence each pair of adjacent slices might have a different estimate of s to pass to partial_pairwise_align.
3. src/paste2/projection/partial_stack_slices_pairwise: Given a sequence of consecutive ST slices and the partial alignments between them, project all slices onto the same 2D coordinate system. 3D reconstruction can be done by assiging a z-value to each slice.

Additionally, src/paste2/PASTE2/partial_pairwise_align_histology uses both gene expression and histological image information for computing the partial alignment matrix.

Installation

PASTE2 is available on PyPI at https://pypi.org/project/paste2/. To install PASTE2, run pip install paste2.

Quick Start

We included a tutorial in this repo (tutorial.ipynb). The tutorial should cover the basics you need to run PASTE2 on your own dataset. Additionally, the documentation of each function is in the source code.

Contact

If you encounter any problem running the software, please contact Xinhao Liu at xl5434@princeton.edu

Reference

Liu, X., Zeira, R., & Raphael, B. J. (2023). Partial alignment of multislice spatially resolved transcriptomics data. Genome Research, 33(7), 1124-1132.