Can single-molecule microscopy be applied to the work of spatiotemporal-omics? Can it will be used to integrate genomics and imaging techniques?

hi, that's an interesting question/vision.

There might be several ways of visualizing gene expression - or mRNA levels -, often utilizing an hybridization technique where a single-stranded and fluorescently labelled DNA probe hybridizes with your RNA of interest. That techniques enables quantification of both the amount (quantity) of the RNA and its localization within the cell. Here is a protocol explaining how you can apply this technique:

https://bio-protocol.org/e3070

another one, RNA paint, which is based on FISH, can visualize chromosomal regions where genes are being transcribed: https://bio-protocol.org/e1914

These are just some examples to visualize transcription in a cell.