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Chen R, Xu J, Wang B, Ding Y, Abdulla A, Li Y, Jiang L, Ding X. SpiDe-Sr: blind super-resolution network for precise cell segmentation and clustering in spatial proteomics imaging. Nat Commun 2024; 15:2708. [PMID: 38548720 PMCID: PMC10978886 DOI: 10.1038/s41467-024-46989-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
Spatial proteomics elucidates cellular biochemical changes with unprecedented topological level. Imaging mass cytometry (IMC) is a high-dimensional single-cell resolution platform for targeted spatial proteomics. However, the precision of subsequent clinical analysis is constrained by imaging noise and resolution. Here, we propose SpiDe-Sr, a super-resolution network embedded with a denoising module for IMC spatial resolution enhancement. SpiDe-Sr effectively resists noise and improves resolution by 4 times. We demonstrate SpiDe-Sr respectively with cells, mouse and human tissues, resulting 18.95%/27.27%/21.16% increase in peak signal-to-noise ratio and 15.95%/31.63%/15.52% increase in cell extraction accuracy. We further apply SpiDe-Sr to study the tumor microenvironment of a 20-patient clinical breast cancer cohort with 269,556 single cells, and discover the invasion of Gram-negative bacteria is positively correlated with carcinogenesis markers and negatively correlated with immunological markers. Additionally, SpiDe-Sr is also compatible with fluorescence microscopy imaging, suggesting SpiDe-Sr an alternative tool for microscopy image super-resolution.
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Grants
- This work was supported by National Key R&D Program of China (2022YFC2601700, 2022YFF0710202) and NSFC Projects (T2122002, 22077079, 81871448), Shanghai Municipal Science and Technology Project(22Z510202478), Shanghai Municipal Education Commission Project(21SG10), Shanghai Jiao Tong University Projects (YG2021ZD19, Agri-X20200101, 2020 SJTU-HUJI), Shanghai Municipal Health Commission Project (2019CXJQ03). Thanks for AEMD SJTU, Shanghai Jiao Tong University Laboratory Animal Center for the supporting.
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Affiliation(s)
- Rui Chen
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiasu Xu
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Boqian Wang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Ding
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Aynur Abdulla
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yiyang Li
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lai Jiang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xianting Ding
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
- State Key Laboratory of Systems Medicine for Cancer, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China.
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