Haematopoietic stem cells (HSCs) arise in the dorsal aorta of the developing mammalian embryo by a process of endothelial-to-haematopoietic transition. Intra-aortic haematopoietic clusters (IAHC) that form during this process are believed to contain the definitive HSC precursors that will sustain all blood lineages throughout the life of an individual. Thus, a thorough understanding of where and when IAHC are formed is paramount to inform protocols to develop HSCs with high multilineage engraftable potential. Methods to image and quantify emerging HSCs in situ rely on protocols developed over a decade ago and require extensive manual counting of clusters. Using tissue clearing, confocal and light-sheet imaging, followed by machine learning analysis, we have developed an imaging pipeline for the segmentation and quantification of IAHC. We apply this pipeline to generate the most comprehensive atlas of emerging haematopoietic stem cells across time and space in the mouse to date. This resource will provide a baseline to which to compare genetic and environmental factors affecting haematopoietic stem cell development.