Superresolved spatial transcriptomics transferred from a histological context

Shu Wang

doi:10.1007/s10489-023-05190-3

2023-12-01

PRE

DOI：10.1007/s10489-023-05190-3

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摘要

En 中文

Spatially resolved transcriptomics (SRT) is a vital technique in biology that allows for gene expression measurement at the resolution of individual spots while preserving spatial information. However, owing to technical limitations, single-spot resolution often includes data from multiple cells, leading to suboptimal results and opportunities for improvement. In this study, we propose a deep learning-based, plug-and-play method for enhancing spot resolution to obtain higher-resolution SRT data. Our approach involves training a convolutional neural network (CNN) model and introducing a shift-predict operation to obtain superresolution spots. Using a human breast cancer SRT dataset, we demonstrate that our method achieves 9 x superresolution, outperforming traditional superresolution techniques. Crucially, our method decreased the mean squared error (MSE) to 1.379 for all genes, 2.287 for tumor-related genes at 4 x superresolution, 1.866 for all genes, and 3.371 for tumor-related genes at 9 x superresolution, reflecting substantial improvements compared to the traditional approaches, including Gaussian RBF, multiquadric RBF, linear RBF, resize-predict, bilinear, and bicubic methods. Furthermore, we verify our method's effectiveness using external and simulated datasets. Our proposed method offers a substantial advancement in SRT by enabling higher-resolution gene expression data generation. By providing a deeper understanding of gene expression patterns and their underlying biological significance, this method contributes to progress in biology and medicine.

Keyword:

Spatially resolved transcriptomics

Superresolution

Histology

Deep learning

期刊

Applied Intelligence

IF:

3.5

论文数:

7.6K

被引数:

1.7W

机构

shanghai jiao tong university

学者数:

15.7W

论文数: 11.7W

被引数: 159

Chinese University of Hong Kong

学者数:

3.4W

论文数: 3.2W

被引数: 5.6W

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