We found a match
Your institution may have rights to this item. Sign in to continue.
- Title
ST-GEARS: Advancing 3D downstream research through accurate spatial information recovery.
- Authors
Xia, Tianyi; Hu, Luni; Zuo, Lulu; Cao, Lei; Zhang, Yunjia; Xu, Mengyang; Lu, Qin; Zhang, Lei; Pan, Taotao; Zhang, Bohan; Ma, Bowen; Chen, Chuan; Guo, Junfu; Shi, Chang; Li, Mei; Liu, Chao; Li, Yuxiang; Zhang, Yong; Fang, Shuangsang
- Abstract
Three-dimensional Spatial Transcriptomics has revolutionized our understanding of tissue regionalization, organogenesis, and development. However, existing approaches overlook either spatial information or experiment-induced distortions, leading to significant discrepancies between reconstruction results and in vivo cell locations, causing unreliable downstream analysis. To address these challenges, we propose ST-GEARS (Spatial Transcriptomics GEospatial profile recovery system through AnchoRS). By employing innovative Distributive Constraints into the Optimization scheme, ST-GEARS retrieves anchors with exceeding precision that connect closest spots across sections in vivo. Guided by the anchors, it first rigidly aligns sections, next solves and denoises Elastic Fields to counteract distortions. Through mathematically proved Bi-sectional Fields Application, it eventually recovers the original spatial profile. Studying ST-GEARS across number of sections, sectional distances and sequencing platforms, we observed its outstanding performance on tissue, cell, and gene levels. ST-GEARS provides precise and well-explainable 'gears' between in vivo situations and in vitro analysis, powerfully fueling potential of biological discoveries. Existing 3D Spatial Transcriptomics reconstruction approaches often overlook spatial information or experiment-induced distortions. Here, authors propose ST-GEARS to bridge the gap between in vivo cell locations and in vitro analysis, accurately recovering spatial profiles.
- Subjects
TRANSCRIPTOMES; BIOMASS energy; LOCATION analysis; MORPHOGENESIS; TISSUES
- Publication
Nature Communications, 2024, Vol 15, Issue 1, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-024-51935-0