This data collection contains tomographic images of vasculature in entire mouse brain, the corresponding blood vessel segmentation, and Python code that transforms the tomographic image into a segmentation and further into a vessel graph representation for analysis. The data were collected and processed at the TOMCAT beamline of the Swiss Light Source in phase-contrast imaging mode. Indian Ink was used as a contrast agent. The original tomographic image data is provided in full resolution, half resolution and quarter resolution (0.65 µm, 1.3 µm and 2.6 µm pixel size, respectively) as 16-bit little endian .raw files. The vessel segmentation is provided in full resolution as a png-compressed image stack.