The mechanical properties of the materials are determined by the size and morphology of fine microscopic features. Quantitative microstructural analysis is a key factor to establish the correlation between the mechanical properties and the thermomechanical treatment under which material condition has been achieved. As such, microstructural analysis is a very important and complex task within the manufacturing sector. Published standards are used for metallographic analysis but typically involve extensive manual interpretation of grain boundaries, resulting in measurements that are slow to produce, difficult to repeat and highly subjective. Computer vision and the evolution of artificial intelligence in the past decade can offer solutions to such problems. Deep learning and digital image processing techniques allow digital microstructural analysis to be automated using a fast and repeatable method. This paper proposes a novel boundary class semantic segmentation approach (BCSS) to identify each phase of the microstructure and additionally estimate the location of the grain boundaries. The BCSS is then combined with more traditional segmentation techniques based on the Watershed Transform to improve the identification and measurement of each feature within the microstructure using a new, hybrid automated digital microstructure analysis approach. The new method is validated on a published dataset of two-phase titanium alloy microstructure pictures captured using a scanning electron microscope. Measurements match the level of accuracy of accepted manual standards, and the method is demonstrated to be more reliable than other automated approaches. The influence of the subjective nature of manual labelling, required to train the proposed network, is also evaluated.