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Spatially resolved transcriptomics (SRT) has evolved rapidly through various technologies, enabling scientists to investigate both morphological contexts and gene expression profiling at single-cell resolution in parallel. SRT data are…

Advances in spatially-resolved transcriptomics (SRT) technologies have propelled the development of new computational analysis methods to unlock biological insights. As the cost of generating these data decreases, these technologies provide…

Genomics · Quantitative Biology 2024-08-02 Boyi Guo , Wodan Ling , Sang Ho Kwon , Pratibha Panwar , Shila Ghazanfar , Keri Martinowich , Stephanie C. Hicks

Spatially Resolved Transcriptomics (SRT) is a cutting-edge technique that captures the spatial context of cells within tissues, enabling the study of complex biological networks. Recent graph-based methods leverage both gene expression and…

Machine Learning · Computer Science 2025-06-24 Yunhak Oh , Junseok Lee , Yeongmin Kim , Sangwoo Seo , Namkyeong Lee , Chanyoung Park

Spatial Transcriptomics (ST) reveals the spatial distribution of gene expression in tissues, offering critical insights into biological processes and disease mechanisms. However, the high cost, limited coverage, and technical complexity of…

Computer Vision and Pattern Recognition · Computer Science 2025-04-22 Yi Niu , Jiashuai Liu , Yingkang Zhan , Jiangbo Shi , Di Zhang , Marika Reinius , Ines Machado , Mireia Crispin-Ortuzar , Jialun Wu , Chen Li , Zeyu Gao

Spatial Transcriptomics (ST) merges the benefits of pathology images and gene expression, linking molecular profiles with tissue structure to analyze spot-level function comprehensively. Predicting gene expression from histology images is a…

Computer Vision and Pattern Recognition · Computer Science 2025-12-01 Chen Zhang , Yilu An , Ying Chen , Hao Li , Xitong Ling , Lihao Liu , Junjun He , Yuxiang Lin , Zihui Wang , Rongshan Yu

Spatial transcriptomics (ST) profiles gene expression across a tissue section while preserving the spatial coordinates. Because current ST technologies typically profile two-dimensional tissue slices, integrating and aligning slices from…

Quantitative Methods · Quantitative Biology 2026-03-20 Yaqi Wu , Jingfeng Wang , Xin Maizie Zhou , Yanxiang Zhao , Zixuan Cang

Spatially resolved transcriptomics (ST) measures gene expression along with the spatial coordinates of the measurements. The analysis of ST data involves significant computation complexity. In this work, we propose gene expression…

Genomics · Quantitative Biology 2022-05-24 Zhuoyan Xu , Kris Sankaran

Spatial transcriptomics (ST) reveals spatial heterogeneity of gene expression, yet its resolution is limited by current platforms. Recent methods enhance resolution via H&E-stained histology, but three major challenges persist: (1)…

Image and Video Processing · Electrical Eng. & Systems 2025-08-12 Xuepeng Liu , Zheng Jiang , Pinan Zhu , Hanyu Liu , Chao Li

Spatial transcriptomics (ST) has revolutionized biomedical research by enabling high resolution gene expression profiling within tissues. However, the high cost and scarcity of high resolution ST data remain significant challenges. We…

Computer Vision and Pattern Recognition · Computer Science 2025-07-24 Yaoyu Fang , Jiahe Qian , Xinkun Wang , Lee A. Cooper , Bo Zhou

Spatial transcriptomics (ST) provides essential spatial context by mapping gene expression within tissue, enabling detailed study of cellular heterogeneity and tissue organization. However, aligning ST data with histology images poses…

Spatial transcriptomics (ST) is a novel technique that simultaneously captures pathological images and gene expression profiling with spatial coordinates. Since ST is closely related to pathological features such as disease subtypes, it may…

Computer Vision and Pattern Recognition · Computer Science 2025-03-11 Kazuya Nishimura , Ryoma Bise , Yasuhiro Kojima

Spatial Transcriptomics is a novel technology that aligns histology images with spatially resolved gene expression profiles. Although groundbreaking, it struggles with gene capture yielding high corruption in acquired data. Given potential…

Computer Vision and Pattern Recognition · Computer Science 2024-09-30 Gabriel Mejia , Daniela Ruiz , Paula Cárdenas , Leonardo Manrique , Daniela Vega , Pablo Arbeláez

Spatial transcriptomics (ST) enables transcriptome-wide profiling while preserving the spatial context of tissues, offering unprecedented opportunities to study tissue organization and cell-cell interactions in situ. Despite recent…

Computer Vision and Pattern Recognition · Computer Science 2026-01-21 Wei Wang , Quoc-Toan Ly , Chong Yu , Jun Bai

Traffic prediction is a cornerstone of modern intelligent transportation systems and a critical task in spatio-temporal forecasting. Although advanced Spatio-temporal Graph Neural Networks (STGNNs) and pre-trained models have achieved…

Machine Learning · Computer Science 2026-01-01 Weilin Ruan , Xilin Dang , Ziyu Zhou , Sisuo Lyu , Yuxuan Liang

The advent of next-generation sequencing-based spatially resolved transcriptomics (SRT) techniques has reshaped genomic studies by enabling high-throughput gene expression profiling while preserving spatial and morphological context.…

Applications · Statistics 2023-12-14 Bencong Zhu , Guanyu Hu , Yang Xie , Lin Xu , Xiaodan Fan , Qiwei Li

Spatial transcriptomics data analysis integrates cellular transcriptional activity with spatial coordinates to identify spatial domains, infer cell-type dynamics, and characterize gene expression patterns within tissues. Despite recent…

Quantitative Methods · Quantitative Biology 2026-03-25 Sean Cottrell , Guo-Wei Wei , Longxiu Huang

Spatial transcriptomics (ST) is a groundbreaking genomic technology that enables spatial localization analysis of gene expression within tissue sections. However, it is significantly limited by high costs and sparse spatial resolution. An…

Image and Video Processing · Electrical Eng. & Systems 2024-07-31 Zhiceng Shi , Shuailin Xue , Fangfang Zhu , Wenwen Min

Spatial transcriptomics (ST) technologies enable gene expression profiling with spatial resolution, offering unprecedented insights into tissue organization and disease heterogeneity. However, current analysis methods often struggle with…

The technology to generate Spatially Resolved Transcriptomics (SRT) data is rapidly being improved and applied to investigate a variety of biological tissues. The ability to interrogate how spatially localised gene expression can lend new…

Quantitative Methods · Quantitative Biology 2021-08-04 Natalie Charitakis , Mirana Ramialison , Hieu T. Nim

Speech super-resolution (SR) reconstructs high-fidelity wideband speech from low-resolution inputs-a task that necessitates reconciling global harmonic coherence with local transient sharpness. While diffusion-based generative models yield…

Sound · Computer Science 2026-01-01 Jiajun Yuan , Xiaochen Wang , Yuhang Xiao , Yulin Wu , Chenhao Hu , Xueyang Lv
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