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Spatial transcriptomics (ST) provides crucial insights into tissue micro-environments, but is limited to its high cost and complexity. As an alternative, predicting gene expression from pathology whole slide images (WSI) is gaining…

Computer Vision and Pattern Recognition · Computer Science 2025-07-01 Mingcheng Qu , Yuncong Wu , Donglin Di , Yue Gao , Tonghua Su , Yang Song , Lei Fan

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 is a technology that captures gene expression levels at different spatial locations, widely used in tumor microenvironment analysis and molecular profiling of histopathology, providing valuable insights into…

Computer Vision and Pattern Recognition · Computer Science 2025-06-11 Junzhuo Liu , Markus Eckstein , Zhixiang Wang , Friedrich Feuerhake , Dorit Merhof

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

In recent years, the advent of spatial transcriptomics (ST) technology has unlocked unprecedented opportunities for delving into the complexities of gene expression patterns within intricate biological systems. Despite its transformative…

Image and Video Processing · Electrical Eng. & Systems 2024-07-12 Wenwen Min , Zhiceng Shi , Jun Zhang , Jun Wan , Changmiao Wang

The rapid advancement of spatial transcriptomics (ST), i.e., spatial gene expressions, has made it possible to measure gene expression within original tissue, enabling us to discover molecular mechanisms. However, current ST platforms…

Computer Vision and Pattern Recognition · Computer Science 2025-11-11 Xiaofei Wang , Stephen Price , Chao Li

Tumour heterogeneity in breast cancer poses challenges in predicting outcome and response to therapy. Spatial transcriptomics technologies may address these challenges, as they provide a wealth of information about gene expression at the…

Image and Video Processing · Electrical Eng. & Systems 2023-09-19 Md Mamunur Rahaman , Ewan K. A. Millar , Erik Meijering

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

With the rapid advancement of Spatial Resolved Transcriptomics (SRT) technology, it is now possible to comprehensively measure gene transcription while preserving the spatial context of tissues. Spatial domain identification and gene…

Genomics · Quantitative Biology 2024-08-14 Donghai Fang , Fangfang Zhu , Dongting Xie , Wenwen Min

Spatial transcriptomics (ST) provides spatially resolved measurements of gene expression, enabling characterization of the molecular landscape of human tissue beyond histological assessment as well as localized readouts that can be aligned…

Computer Vision and Pattern Recognition · Computer Science 2026-02-17 Konstantin Hemker , Andrew H. Song , Cristina Almagro-Pérez , Guillaume Jaume , Sophia J. Wagner , Anurag Vaidya , Nikola Simidjievski , Mateja Jamnik , Faisal Mahmood

The rapid development of spatial transcriptomics(ST) enables the measurement of gene expression at spatial resolution, making it possible to simultaneously profile the gene expression, spatial locations of spots, and the matched…

Artificial Intelligence · Computer Science 2024-06-19 Changxi Chi , Hang Shi , Qi Zhu , Daoqiang Zhang , Wei Shao

Spatial transcriptomics (ST) provides high-resolution pathological images and whole-transcriptomic expression profiles at individual spots across whole-slide scales. This setting makes it an ideal data source to develop multimodal…

Computer Vision and Pattern Recognition · Computer Science 2024-11-27 Yuxiang Lin , Ling Luo , Ying Chen , Xushi Zhang , Zihui Wang , Wenxian Yang , Mengsha Tong , Rongshan Yu

Spatial Transcriptomics (ST) allows a high-resolution measurement of RNA sequence abundance by systematically connecting cell morphology depicted in Hematoxylin and Eosin (H&E) stained histology images to spatially resolved gene…

Computer Vision and Pattern Recognition · Computer Science 2025-03-21 Sichen Zhu , Yuchen Zhu , Molei Tao , Peng Qiu

Spatial transcriptomics (ST) is a novel technology that enables the observation of gene expression at the resolution of individual spots within pathological tissues. ST quantifies the expression of tens of thousands of genes in a tissue…

Machine Learning · Computer Science 2025-11-25 Kaito Shiku , Kazuya Nishimura , Shinnosuke Matsuo , Yasuhiro Kojima , Ryoma Bise

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 enables simultaneous measurement of gene expression and tissue morphology, offering unprecedented insights into cellular organization and disease mechanisms. However, the field lacks comprehensive benchmarks for…

The recent advancement of spatial transcriptomics (ST) allows to characterize spatial gene expression within tissue for discovery research. However, current ST platforms suffer from low resolution, hindering in-depth understanding of…

Image and Video Processing · Electrical Eng. & Systems 2025-11-05 Xiaofei Wang , Xingxu Huang , Stephen J. Price , Chao Li

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 provides an unprecedented perspective for deciphering tissue spatial heterogeneity. However, high-resolution spatial transcriptomic technology remains constrained by limited gene coverage, technical complexity, and…

Biomolecules · Quantitative Biology 2026-05-19 Xinlei Huang , Weihao Dai , Zijun Qin , Xin Yu , Di Wang , Yanran Liu , Lixin Cheng , Xubin Zheng

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
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