<p>Quick and accurate segmentation and object detection of the biomedical image is the starting point of most disease analysis and understanding of biological processes in medical research. It will enhance drug development and advance medical treatment, especially in cancer-related diseases. However, identifying the objects in the CT or MRI images and labeling them usually takes time even for an experienced person. Currently, there is no automatic detection technique for nucleus identification, pneumonia detection, and fetus brain segmentation. Fortunately, as the successful application of artificial intelligence (AI) in image processing, many challenging tasks are easily solved with deep convolutional neural networks. In light of this, in this thesis, the deep learning based object detection and segmentation methods were implemented to perform the nucleus segmentation, lung segmentation, pneumonia detection, and fetus brain segmentation. The semantic segmentation is achieved by the customized U-Net model, and the instance localization is achieved by Faster R-CNN. The reason we choose U-Net is that such a network can be trained end-to-end, which means the architecture of this network is very simple, straightforward and fast to train. Besides, for this project, the availability of the dataset is limited, which makes U-Net a more suitable choice. We also implemented the Faster R-CNN to achieve the object localization. Finally, we evaluated the performance of the two models and further compared the pros and cons of them. The preliminary results show that deep learning based technique outperforms all existing traditional segmentation algorithms. </p>