Schematic diagram for spatial transcriptomics analysis at subcellular resolution. (A) For spatial data at subcellular resolution, each dot typically represents a single transcript or, alternatively, a spatial unit that is well below the cell size. (B) The location of each transcript, along with its gene identity, can be used as input to try and segment each cell. (C) Individual transcripts can be colocalized with other transcripts (orange and blue) or with itself (green) or can be found at specific subcellular structures (pink at membrane). (D) Transcription dynamics from individual or multiple genes can be inferred from the location of transcripts. Here nascent transcripts are typically found in the nucleus (blue), whereas processed transcripts are found in the cytoplasm (orange). The ratio between the two can provide an estimate for the RNA velocity. Examples for each analysis are provided on the right of each panel using the seqFISH+ data set from the mouse somatosensory cortex.
