Bone metastases are one of the most dangerous consequences of breast cancer. Early diagnosis and treatment would slow down the development of the disease and increase the survival rates of patients. Bone micro-vasculature is believed to play a major role in the development of bone metastases. It could be used for both diagnosis and as a therapeutic target. Synchrotron radiation micro-computed tomography (SR-µCT) with a contrast agent of blood vessels has been used to analyze the bone vasculature both in healthy and in metastatic bone. However, few studies have investigated the local features of blood vessels around metastases so far. For this purpose, the metastases first need to be automatically segmented. This is a challenging task, however, since the metastases do not contribute a specific contrast to the three-dimensional (3D) SR-µCT images. Here, we propose a new method for the simultaneous segmentation of bone, blood vessels, and metastases from contrast enhanced 3D SR-µCT images based on the nnU-Net architecture. In this study, we showed that only minimal training data was required to achieve a high quality of segmentation. The proposed method allowed for the automatic segmentation of metastases and provided an improved segmentation of bone and blood vessels compared to previous methods while being much more efficient to apply once trained. Further, the automatic segmentation allowed for the measurement of vascular metastases interdistance and to restrict measurements to volumes of interest around the metastases. Finally, we quantitatively analyzed blood vessel parameters locally around metastases. This allowed for the demonstration that a combined anti-angiogenic treatment significantly decreased the volume and thickness of blood vessels close to metastases. The proposed method showed the capacity of the method to reveal new aspects of the blood vessel structure interaction with metastases. This could be further used to both define new targets for precocious detection of metastases as well as to study the kinetics of metastasis development in bone and the action of drugs on this process.