PXD050123
PXD050123 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | SpiDe-Sr: blind super-resolution network for precise cell segmentation and clustering in spatial proteomics imaging |
Description | 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. |
HostingRepository | iProX |
AnnounceDate | 2024-02-25 |
AnnouncementXML | Submission_2024-04-01_19:50:25.804.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Rui Chen |
SpeciesList | scientific name: Homo sapiens; NCBI TaxID: 9606; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive HF-X |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2024-02-25 21:50:34 | ID requested | |
1 | 2024-02-25 21:52:18 | announced | |
2 | 2024-04-01 00:51:22 | announced | 2024-04-01: Update information. |
⏵ 3 | 2024-04-01 19:50:26 | announced | 2024-04-01: Update information. 2024-04-02: Update publication information. |
Publication List
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, 15(1):2708(2024) [pubmed] |
Keyword List
submitter keyword: Proteomics raw data, Raw data of imaging mass cytometry (IMC) |
Contact List
Xianting Ding | |
---|---|
contact affiliation | Shanghai Jiao Tong University |
contact email | dingxianting@sjtu.edu.cn |
lab head | |
Rui Chen | |
contact affiliation | Shanghai Jiao Tong University |
contact email | chenrui115@sjtu.edu.cn |
dataset submitter |
Full Dataset Link List
iProX dataset URI |