StereoCell: a highly accurate single-cell gene expression processing software for high-resolution spatial transcriptomics
IDSTT0000027(Source: STOmics DB)
STOmics technology:BGI Stereomics Stereo-Seq
Organism(s):
Data type:STOmics
Sample scope:Multiisolate
Summary:Owing to recent advances in resolution and field-of-view, spatially resolved sequencing has emerged as a cutting-edge technology that provides a technical foundation for the interpretation of large tissues at the single-cell level. To generate accurate single-cell spatial gene expression profiles from high-resolution spatial omics data and associated images, a powerful tool is required. Here we present StereoCell, an image-facilitated one-stop software for high-resolution and large field-of-view spatial transcriptomic data . StereoCell provides a comprehensive and systematic platform for the generation of high-confidence single-cell spatial gene expression profiles, which includes image stitching, image registration, tissue segmentation, nuclei segmentation and molecule labeling. StereoCell has been applied to obtain reliable single-cell spatial gene expression profiles for mouse embryo and continuous mouse brain slices in previous published works. StereoCell is user-friendly and doesn’t require a specific level of expertise. For mouse brain dataset (131,990,020 genes and 117 tiles), StereoCell can be carried out in 4.8h on a server with 40-core CPU, 128GB of RAM and 24GB of GPU.
Contributor(s):Qiang Kang.
Publication(s):
  • Mei Li, Huanlin Liu, Min Li, Shuangsang Fang, Qiang Kang et al. StereoCell enables highly accurate single-cell segmentation for spatial transcriptomics.
Submitter:Kang Qiang,BGI-Shenzhen
Release date:2023-03-29
Updated:2023-07-14
Statistics:
  • Sample: 2
  • Tissue Section: 2
Datasize:3.22GB

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