PXD050123

PXD050123 is an original dataset announced via ProteomeXchange.

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

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.

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]

submitter keyword: Proteomics raw data, Raw data of imaging mass cytometry (IMC)

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

iProX dataset URI