Automated lateral sectioning for Knife-Edge Scanning Microscopy

Recent advances in high-throughput microscopy are used to acquire large-scale anatomical information at the microscopic level. One of these methods, known as knife-edge scanning microscopy (KESM), allows large volumes of tissue to be imaged using physical sectioning. This method has been limited, however, by constraints on the field of view of the objective and the need to prevent damage to tissue before it is imaged. In this paper, we describe a simple sectioning algorithm we use to overcome these constraints on tissue size. By maintaining a height field of the tissue surface, we are able to cut lateral sections while minimizing damage to un-imaged tissue. Although lateral sectioning introduces some deformation and tissue damage at the interface of the sections, the damage is minimal and the deformations can be compensated for using affine transformations.