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Paste 3

Paste 3 (Paste + Paste 2) is a Python package and NAPARI plugin that provides advanced alignment methods of Spatial Transcriptonomics (ST) data as detailed in the following publications:

1. PASTE

Zeira, R., Land, M., Strzalkowski, A., et al. Alignment and integration of spatial transcriptomics data. Nat Methods, 19, 567–575 (2022).

Read the publication
Original PASTE code

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2. PASTE2

Liu X, Zeira R, Raphael BJ. Partial alignment of multislice spatially resolved transcriptomics data. Genome Res. 2023 Jul; 33(7):1124-1132. Read the publication
Original PASTE2 code

The motivation behind PASTE3 is to provide a NAPARI plugin for practitioners to experiment with both PASTE and PASTE2 at an operational level, as well as provide a common codebase for future development of ST alignment algorithms. (Paste-N..)

PASTE3 is built on pytorch and can leverage a GPU for performance if available, though it is able to run just fine in the absence of a GPU, on all major platforms.

Auto-generated documentation for the PASTE3 package is available here.

Additional examples and the code to reproduce the original PASTE paper's analyses are available here. Preprocessed datasets used in the paper can be found on zenodo.

Overview

The PASTE series of algorithms provide computational methods that leverage both gene expression similarity and spatial distances between spots to align and integrate spatial transcriptomics data. In particular, there are two modes of operation:

1. Pairwise-Alignment: align spots between successive pairs of slices.
2. Center-Alignment: infer a center slice (low sparsity, low variance) and align all slices with respect to this center slice.

Installation

The easiest way is to install PASTE3 is using pip:

pip install git+https://github.com/raphael-group/paste3.git

Developers who wish to work with paste3 in Python will likely want to review the detailed installation page.

Getting Started

If you intend to use PASTE3 as a napari plugin, install paste3 in a python environment that has napari installed, or install napari after having installed paste3 as above.

pip install napari

Open one of the sample datasets we provide (File->Open Sample->Paste3->SCC Patient..) and then select one of the two modes of PASTE3 operations (Plugins->Paste3->Center Align or Plugins->Paste3->Pairwise Align).

Your own datasets can be used if they're in the .h5ad format, with each file denoting a single slice. With the default parameters, alignment should take a couple of minutes, though you have the option of changing these to suit your needs.

If you intend to use PASTE3 programmatically in your Python code, follow along the Getting Started tutorial.