Bone Scan Index (BSI) is an image biomarker for quantifying bone metastasis of cancers. To compute BSI, not only the hotspots (metastasis) but also the bones have to be segmented. Most related research focus on binary classification in bone scintigraphy: having metastasis or none. Rare studies focus on pixel-wise segmentation. This study compares three advanced convolutional neural network (CNN) based models to explore bone segmentation on a dataset in-house. The best model is Mask R-CNN, which reaches the precision, sensitivity, and F1-score: 0.93, 0.87, 0.90 for prostate cancer patients and 0.92, 0.86, and 0.88 for breast cancer patients, respectively. The results are the average of 10-fold cross-validation, which reveals the reliability of clinical use on bone segmentation.