{ "cells": [ { "cell_type": "markdown", "id": "c57e9685-eb1d-46bb-ab38-12ff55cefb1a", "metadata": {}, "source": [ "# Spatial Alignment\n", "\n", "Integrative analysis of spatially resolved transcriptomics datasets empowers a deeper understanding of complex biological systems. However, integrating multiple tissue sections presents challenges for batch effect removal, particularly when the sections are measured by various technologies or collected at different times. Here, we propose **Spatial Alignment**, an unsupervised contrastive learning model that employs the expression of all measured genes and the spatial location of cells, to integrate multiple tissue sections. It enables the joint downstream analysis of multiple datasets not only in low-dimensional embeddings but also in the reconstructed full expression space. In benchmarking analysis, spatiAlign outperforms state-of-the-art methods in learning joint and discriminative representations for tissue sections, each potentially characterized by complex batch effects or distinct biological characteristics\n", "\n", "After alignment, we will get a new expression matrix and a reduced dimensional matrix, we can use them to do others analysis such as Neighbors, UMAP, Cluster, etc." ] }, { "cell_type": "markdown", "id": "8cceaa02", "metadata": {}, "source": [ "
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