Dataset annotation is a time and labor-intensive task and an integral requirement for training and testing deep learning models. The segmentation of images in life science microscopy requires annotated image datasets for object detection tasks such as instance segmentation. Although the amount of annotated image data has been steadily reduced due to methods such as data augmentation, the process of manual or semi-automated data annotation is the most labor and cost intensive task in the process of cell nuclei segmentation with deep neural networks. In this work we propose a system to fully automate the annotation process of a custom fluorescent cell nuclei image dataset. By that we are able to reduce nuclei labelling time by up to 99.5%. The output of our system provides high quality training data for machine learning applications to identify the position of cell nuclei in microscopy images. Our experiments have shown that the automatically annotated dataset provides coequal segmentation performance compared to manual data annotation. In addition, we show that our system enables a single workflow from raw data input to desired nuclei segmentation and tracking results without relying on pre-trained models or third-party training datasets for neural networks.