Methods and software for creating a 3D image from images of multiple histological sections and for mapping anatomical information from a reference atlas to a histological image

Methods and software assisting a user in working with images of histological sections to increase the user's productivity and decrease the need for extensive expertise in anatomy. In some embodiments, the methods include methods of assisting a user in creating a 3D volume image of a tissue block from a series of images of histological sections taken from the tissue block. In some embodiments, the methods include methods of automatedly registering a live-view or stored histological section image to a tissue block atlas. In some embodiments, the methods include methods of annotating a histological section image with information from a tissue block atlas based on user input(s) associated with the tissue block atlas. In some embodiments, the methods include methods of automatedly controlling operation of an imaging modality, such as an optical microscope, based on user input(s) associated with a tissue block atlas. These and other methods may be embodied in various configurations of software.