Methods and apparatuses for assessing oral health and automatically providing diagnosis of one or more oral diseases. Described herein are intraoral scanning methods and apparatuses for collecting and analyzing image data and to detect and visualize features within image data that are indicative of oral diseases or conditions, such as gingival inflammation or oral cancer. These methods and apparatuses may be used for identifying and evaluating lesions, redness and inflammation in soft tissue and caries and cracks in the teeth. The methods can include training a machine learning model and using the trained machine learning model to provide a diagnosis of an oral disease or condition based on image data collected using multiple scanning modes of an intraoral scanner.