High-throughput profiling of in situ gene expression represents a major advance towards the systematic understanding of tissue complexity. Applied with enough capture area and high sample throughput it will help to define the spatio-temporal dynamics of gene expression in tissues and organisms. Yet, current technologies have considerable bottlenecks that limit widespread application. We have combined DNA nanoball (DNB) patterned array chips and in situ RNA capture to develop Stereo-seq (SpaTial Enhanced REsolution Omics-sequencing). This approach allows high sample throughput transcriptomic profiling of histological sections at unprecedented (nanoscale) resolution with areas expandable to centimeter scale, high sensitivity and homogenous capture rate. As proof of principle, we have applied Stereo-seq to study the kinetics and directionality of transcriptional variation in embryogenesis. We used this information to gain insight into the molecular basis of regional specification and cell fate diversification. Our panoramic atlas constitutes an essential resource to investigate longstanding questions concerning normal and abnormal development.