Please read Dr. Wei’s article in Bioinformatics titled, “Hidden Markov random field models for cell-type assignment of spatially resolved transcriptomics.“
Spatially resolved transcriptomics (SRT) profiles gene expression at high resolution while tracking tissue locations of cells. These technologies have greatly accelerated biomedical studies. Mainstream SRT technology can be grouped into two main categories. One is the in situ hybridization or sequencing-based technologies with single-cell resolution, such as seqFISH, seqFISH+, and MERFISH. These technologies quantify gene expressions at single-cell resolution, but with only tens to hundreds of genes. Another category is spatial barcoding-based sequencing technologies, including SLIDE-seq, SLIDE-seq V2, and 10× Visium (10×Genomics). These methods measure the whole transcriptome in spots that contain dozens of cells. To read the full article.
Hidden Markov random field models for cell-type assignment of spatially resolved transcriptomics. Zhong C, Tian T, Wei Z. 2023 Nov 1;39(11):btad641. PMID: 37944045 PMCID: PMC10640398 DOI: 10.1093/bioinformatics/btad641