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scSLAT: single cell spatial alignment tools

scSLAT package implements the SLAT (Spatially-Linked Alignment Tool) model, which aims to align heterogeneous single cell spatial data fast and accurately. scSLAT works well on various spatial technologies (such as Visium, MERFISH, Stereo-seq, seqFISH, Xenium) and can extend to large datasets easily.

Model architecture

Key applications of scSLAT

  1. Heterogeneous alignment: as the first method designed for heterogeneous spatial alignment, scSLAT enables

    • Cross technologies alignment: Stereo-seq and MERFISH, Visium and Xenium, …

    • Multi modalities alignment: spatial-ATAC-seq and Stereo-seq (with our previous work scglue).

    • Defining development changes: revealing spatial-temporal changes in time-series developmental datasets.

  2. Atlas alignment: precisely align large single cell spatial atlas (200,000+ cells) in 3 minutes.

  3. 3D reconstruction: align multiple continuous spatial slices in parallel to rebuild 3D structure.

Alignment result

Getting started with scSLAT

To get started with scSLAT, check out our installation guide and tutorials.

Contributing to scSLAT

Single-cell spatial omics is still developing rapidly. We are happy about your contributions! Please submit Pull requests on our Github Repo. We think your contribution will make a big difference to community!