There are several powerful methods for analysing single cells extracted from tissues, such as flow cytometry, single-cell RNA sequencing and single-cell ATAC sequencing. However, it is widely recognized that certain cell types cannot be easily isolated intact from tissues. In addition, these methods cannot offer insights into the vital extracellular matrix of tissues and organs, nor can they shed light on cell–cell interactions and spatial organization, which relay critical information in both normal and pathological conditions.