Fluorescence in situ hybridization (FISH) is widely used to obtain information about transcript copy number and subcellular localization in single cells. However, current approaches do not readily scale to the analysis of whole transcriptomes. Here we show that branched DNA technology combined with automated liquid handling, high-content imaging and quantitative image analysis allows highly reproducible quantification of transcript abundance in thousands of single cells at single-molecule resolution. In addition, it allows extraction of a multivariate feature set quantifying subcellular patterning and spatial properties of transcripts and their cell-to-cell variability. This has multiple implications for the functional interpretation of cell-to-cell variability in gene expression and enables the unbiased identification of functionally relevant in situ signatures of the transcriptome without the need for perturbations. Because this method can be incorporated in a wide variety of high-throughput image-based approaches, we expect it to be broadly applicable.