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The advancement of Spatial Transcriptomics (ST) has facilitated the spatially-aware profiling of gene expressions based on histopathology images. Although ST data offers valuable insights into the micro-environment of tumors, its…

Computer Vision and Pattern Recognition · Computer Science 2024-12-23 Hongyi Wang , Xiuju Du , Jing Liu , Shuyi Ouyang , Yen-Wei Chen , Lanfen Lin

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) enables the visualization of gene expression within the context of tissue morphology. This emerging discipline has the potential to serve as a foundation for developing tools to design precision medicines.…

Image and Video Processing · Electrical Eng. & Systems 2024-11-12 Shivam Kumar , Samrat Chatterjee

Recent advances in multi-modal AI have demonstrated promising potential for generating the currently expensive spatial transcriptomics (ST) data directly from routine histology images, offering a means to reduce the high cost and…

Computer Vision and Pattern Recognition · Computer Science 2025-08-21 Junchao Zhu , Ruining Deng , Junlin Guo , Tianyuan Yao , Juming Xiong , Chongyu Qu , Mengmeng Yin , Yu Wang , Shilin Zhao , Haichun Yang , Daguang Xu , Yucheng Tang , Yuankai Huo

Advances in spatial transcriptomics (ST) technologies enable systematic molecular characterization of tumor microenvironment, tumor gradients and gene regulatory networks. Cancer progression is known to vary along pathological gradients,…

Spatial Transcriptomics (ST) provides spatially resolved gene expression profiles within intact tissue architecture, enabling molecular analysis in histological context. However, the high cost, limited throughput, and restricted data…

Machine Learning · Computer Science 2026-03-31 Yaoyu Fang , Jiahe Qian , Xinkun Wang , Lee A. Cooper , Bo Zhou

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

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) 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) 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) 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

Spatial Transcriptomics (ST) enables the measurement of gene expression while preserving spatial information, offering critical insights into tissue architecture and disease pathology. Recent developments have explored the use of…

Computer Vision and Pattern Recognition · Computer Science 2026-05-20 Hai Dang Nguyen , Nguyen Dang Huy Pham , The Minh Duc Nguyen , Dac Thai Nguyen , Hang Thi Nguyen , Duong M. Nguyen

Spatial transcriptomics (ST) enables gene expression mapping within anatomical context but remains costly and low-throughput. Hematoxylin and eosin (H\&E) staining offers rich morphology yet lacks molecular resolution. We present…

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…

The effective extraction of spatial-angular features plays a crucial role in light field image super-resolution (LFSR) tasks, and the introduction of convolution and Transformers leads to significant improvement in this area. Nevertheless,…

Image and Video Processing · Electrical Eng. & Systems 2025-12-02 Zeke Zexi Hu , Xiaoming Chen , Vera Yuk Ying Chung , Yiran Shen

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

The rapid development of digital pathology and modern deep learning has facilitated the emergence of pathology foundation models that are expected to solve general pathology problems under various disease conditions in one unified model,…

Computer Vision and Pattern Recognition · Computer Science 2025-07-10 Yutong Sun , Sichen Zhu , Peng Qiu

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

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

Spatial transcriptomics reveals gene expression patterns within tissue context, enabling precision oncology applications such as treatment response prediction, but its high cost and technical complexity limit clinical adoption. Predicting…

Computer Vision and Pattern Recognition · Computer Science 2025-08-04 Won June Cho , Hongjun Yoon , Daeky Jeong , Hyeongyeol Lim , Yosep Chong
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