Spotiphy enables single-cell spatial whole transcriptomics across an entire section
Year: 2025
Type: article
Abstract: Spatial transcriptomics (ST) has advanced our understanding of tissue regionalization by enabling the visualization of gene expression within whole-tissue sections, but current approaches remain plagued by the challenge of achieving single-cell resolution without sacrificing whole-genome coverage. Here we present Spotiphy (spot imager with pseudo-single-cell-resolution histology), a computational toolkit that transforms sequencing-based ST data into single-cell-resolved whole-transcriptome images. Spotiphy delivers the most precise cellular proportions in extensive benchmarking evaluations. Spotiphy-derived inferred single-cell profiles reveal astrocyte and disease-associated microglia regional specifications in Alzheimer's disease and healthy mouse brains. Spotiphy identifies multiple spatial domains and alterations in tumor-tumor microenvironment interactions in human breast ST data. Spotiphy bridges the information gap and enables visualization of cell localization and transcriptomic profiles throughout entire sections, offering highly informative outputs and an innovative spatial analysis pipeline for exploring complex biological systems.
Source: Nature Methods
Authors: Jiyuan Yang, Ziqian Zheng, Yun Jiao, Kaiwen Yu, Sheetal Bhatara, Xu Yang, Sivaraman Natarajan, Jiahui Zhang, Qingfei Pan, John Easton, Koon-Kiu Yan, Junmin Peng, Kaibo Liu, Jiyang Yu
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $12,690
Awards: Intracellular and Intercellular Network Rewiring and Hidden Driver Inference from Single-Cell Data, G3027589626, G3164329303, Dissecting neuron-microglia-astrocyte interaction in AD pathogenesis, G4006632108, G4123171607, Dissecting neuron-microglia-astrocyte interaction in AD pathogenesis, G841158765, Investigating the Molecular Determinants Driving Response and Resistance to HDAC6 Targeted Therapy in Breast Cancer, Clonal Therapy for Pediatric T-cell Acute Lymphoblastic Leukemia, Enabling immunotherapy for high-risk Group 3 medulloblastoma via systems immunology
OpenAlex ID: W4408372348