Three-dimensional single-cell transcriptome imaging of thick tissues
Multiplexed error-robust fluorescence in situ hybridization (MERFISH) allows genome-scale imaging of RNAs in individual cells in intact tissues. To date, MERFISH has been applied to image thin-tissue samples of ~10 µm thickness. Here, we present a thick-tissue three-dimensional (3D) MERFISH imaging...
| Published in: | eLife |
|---|---|
| Main Authors: | Rongxin Fang, Aaron Halpern, Mohammed Mostafizur Rahman, Zhengkai Huang, Zhiyun Lei, Sebastian J Hell, Catherine Dulac, Xiaowei Zhuang |
| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications Ltd
2024-12-01
|
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/90029 |
Similar Items
Comparison of spatial transcriptomics technologies using tumor cryosections
by: Anne Rademacher, et al.
Published: (2025-06-01)
by: Anne Rademacher, et al.
Published: (2025-06-01)
Multiplexed spatial transcriptomics methods and the application of expansion microscopy
by: Andra Fortner, et al.
Published: (2024-07-01)
by: Andra Fortner, et al.
Published: (2024-07-01)
Systematic benchmarking of computational methods to identify spatially variable genes
by: Zhijian Li, et al.
Published: (2025-09-01)
by: Zhijian Li, et al.
Published: (2025-09-01)
Protocol optimization improves the performance of multiplexed RNA imaging
by: Josh J. Luce, et al.
Published: (2025-08-01)
by: Josh J. Luce, et al.
Published: (2025-08-01)
Enablers and challenges of spatial omics, a melting pot of technologies
by: Theodore Alexandrov, et al.
Published: (2023-11-01)
by: Theodore Alexandrov, et al.
Published: (2023-11-01)
Integrating physiological and transcriptomic analyses at the single-neuron level
by: Haruya Yagishita, et al.
Published: (2025-05-01)
by: Haruya Yagishita, et al.
Published: (2025-05-01)
Mammalian gene expression variability is explained by underlying cell state
by: Robert Foreman, et al.
Published: (2020-02-01)
by: Robert Foreman, et al.
Published: (2020-02-01)
The Advancement and Application of the Single-Cell Transcriptome in Biological and Medical Research
by: Kongwei Huang, et al.
Published: (2024-06-01)
by: Kongwei Huang, et al.
Published: (2024-06-01)
Current state and future prospects of spatial biology in colorectal cancer
by: Francisco G. Carranza, et al.
Published: (2024-12-01)
by: Francisco G. Carranza, et al.
Published: (2024-12-01)
A New Tool to Decrease Interobserver Variability in Biomarker Annotation in Solid Tumor Tissue for Spatial Transcriptomic Analysis
by: Sravya Palavalasa, et al.
Published: (2025-07-01)
by: Sravya Palavalasa, et al.
Published: (2025-07-01)
iIMPACT: integrating image and molecular profiles for spatial transcriptomics analysis
by: Xi Jiang, et al.
Published: (2024-06-01)
by: Xi Jiang, et al.
Published: (2024-06-01)
Integration of histopathological image features and multi-dimensional omics data in predicting molecular features and survival in glioblastoma
by: Yeqian Huang, et al.
Published: (2025-04-01)
by: Yeqian Huang, et al.
Published: (2025-04-01)
How is spatial transcriptomics influencing cancer research and diagnostics?
by: Annie Coulson
Published: (2022-11-01)
by: Annie Coulson
Published: (2022-11-01)
Computational modeling for deciphering tissue microenvironment heterogeneity from spatially resolved transcriptomics
by: Chuanchao Zhang, et al.
Published: (2024-12-01)
by: Chuanchao Zhang, et al.
Published: (2024-12-01)
Detection of differentially expressed genes in spatial transcriptomics data by spatial analysis of spatial transcriptomics: A novel method based on spatial statistics
by: Zhihua Qiu, et al.
Published: (2022-11-01)
by: Zhihua Qiu, et al.
Published: (2022-11-01)
Spatial metabolomics and transcriptomics reveal cell type-specific dynamics in the placenta of patients with late-onset preeclampsia
by: Xiaowei Wei, et al.
Published: (2025-10-01)
by: Xiaowei Wei, et al.
Published: (2025-10-01)
Recent advances in spatially variable gene detection in spatial transcriptomics
by: Sikta Das Adhikari, et al.
Published: (2024-12-01)
by: Sikta Das Adhikari, et al.
Published: (2024-12-01)
Spatial Transcriptomic Technologies
by: Tsai-Ying Chen, et al.
Published: (2023-08-01)
by: Tsai-Ying Chen, et al.
Published: (2023-08-01)
A guidebook of spatial transcriptomic technologies, data resources and analysis approaches
by: Liangchen Yue, et al.
Published: (2023-01-01)
by: Liangchen Yue, et al.
Published: (2023-01-01)
Potential Molecular Mechanisms of Alzheimer’s Disease from Genetic Studies
by: Martin Nwadiugwu, et al.
Published: (2023-04-01)
by: Martin Nwadiugwu, et al.
Published: (2023-04-01)
Genomic and transcriptomic resources for assassin flies including the complete genome sequence of Proctacanthus coquilletti (Insecta: Diptera: Asilidae) and 16 representative transcriptomes
by: Rebecca B. Dikow, et al.
Published: (2017-01-01)
by: Rebecca B. Dikow, et al.
Published: (2017-01-01)
Spatial transcriptomics: recent developments and insights in respiratory research
by: Wen-Jia Wang, et al.
Published: (2023-08-01)
by: Wen-Jia Wang, et al.
Published: (2023-08-01)
Single-cell spatial transcriptomics in cardiovascular development, disease, and medicine
by: Songjie Han, et al.
Published: (2024-11-01)
by: Songjie Han, et al.
Published: (2024-11-01)
Next Generation Digital Pathology: Emerging Trends and Measurement Challenges for Molecular Pathology
by: Alex Dexter, et al.
Published: (2022-09-01)
by: Alex Dexter, et al.
Published: (2022-09-01)
SC2Spa: a deep learning based approach to map transcriptome to spatial origins at cellular resolution
by: Linbu Liao, et al.
Published: (2025-06-01)
by: Linbu Liao, et al.
Published: (2025-06-01)
LETSmix: a spatially informed and learning-based domain adaptation method for cell-type deconvolution in spatial transcriptomics
by: Yangen Zhan, et al.
Published: (2025-02-01)
by: Yangen Zhan, et al.
Published: (2025-02-01)
An integrated approach for analyzing spatially resolved multi-omics datasets from the same tissue section
by: Thao Tran, et al.
Published: (2025-07-01)
by: Thao Tran, et al.
Published: (2025-07-01)
Comparative genomic and transcriptomic analyses provide new insight into symbiotic host specificity
by: Songli Yuan, et al.
Published: (2024-07-01)
by: Songli Yuan, et al.
Published: (2024-07-01)
pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging
by: Xavier Devos, et al.
Published: (2024-02-01)
by: Xavier Devos, et al.
Published: (2024-02-01)
WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations
by: Yongzhi Yang, et al.
Published: (2019-02-01)
by: Yongzhi Yang, et al.
Published: (2019-02-01)
Clinical challenges of tissue preparation for spatial transcriptome
by: Xiaoxia Liu, et al.
Published: (2022-01-01)
by: Xiaoxia Liu, et al.
Published: (2022-01-01)
High-resolution diffusion magnetic resonance imaging and spatial-transcriptomic in developing mouse brain
by: Xinyue Han, et al.
Published: (2024-08-01)
by: Xinyue Han, et al.
Published: (2024-08-01)
Multi-slice spatial transcriptome domain analysis with SpaDo
by: Bin Duan, et al.
Published: (2024-03-01)
by: Bin Duan, et al.
Published: (2024-03-01)
Spatial transcriptomics herald a new era of transcriptome research
by: Dominik Saul, et al.
Published: (2023-05-01)
by: Dominik Saul, et al.
Published: (2023-05-01)
Genome-wide spatial expression profiling in formalin-fixed tissues
by: Eva Gracia Villacampa, et al.
Published: (2021-12-01)
by: Eva Gracia Villacampa, et al.
Published: (2021-12-01)
Spatial and Single‐Cell Transcriptomics Unraveled Spatial Evolution of Papillary Thyroid Cancer
by: Guangzhe Zheng, et al.
Published: (2025-01-01)
by: Guangzhe Zheng, et al.
Published: (2025-01-01)
Benchmarking multi-slice integration and downstream applications in spatial transcriptomics data analysis
by: Kejing Dong, et al.
Published: (2025-09-01)
by: Kejing Dong, et al.
Published: (2025-09-01)
stBERT: A Pretrained Model for Spatial Domain Identification of Spatial Transcriptomics
by: Ziheng Wang, et al.
Published: (2024-01-01)
by: Ziheng Wang, et al.
Published: (2024-01-01)
Advances and Challenges in Spatial Transcriptomics for Developmental Biology
by: Kyongho Choe, et al.
Published: (2023-01-01)
by: Kyongho Choe, et al.
Published: (2023-01-01)
Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues
by: Emelie Berglund, et al.
Published: (2020-04-01)
by: Emelie Berglund, et al.
Published: (2020-04-01)
Similar Items
-
Comparison of spatial transcriptomics technologies using tumor cryosections
by: Anne Rademacher, et al.
Published: (2025-06-01) -
Multiplexed spatial transcriptomics methods and the application of expansion microscopy
by: Andra Fortner, et al.
Published: (2024-07-01) -
Systematic benchmarking of computational methods to identify spatially variable genes
by: Zhijian Li, et al.
Published: (2025-09-01) -
Protocol optimization improves the performance of multiplexed RNA imaging
by: Josh J. Luce, et al.
Published: (2025-08-01) -
Enablers and challenges of spatial omics, a melting pot of technologies
by: Theodore Alexandrov, et al.
Published: (2023-11-01)
