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Cell segmentation and gene imputation for imaging-based spatial transcriptomics

Zhong, Y.; Ren, X.

2023-10-30 bioinformatics
10.1101/2023.10.26.564185 bioRxiv
Show abstract

Imaging-based spatial transcriptomics technologies are revolutionary tools for biomedical investigation, but the power is currently limited by small number of measured genes and tricky cell segmentation. Here we introduce RedeFISH to simultaneously conduct cell segmentation and gene imputation for imaging-based spatial transcriptomics with the aid of single-cell RNA sequencing data. Extensive benchmarking across various spatial platforms and tissue types shows the validity and power of the cell-segmented, whole-transcriptome spatial data generated by RedeFISH.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.