Combining light sheet microscopy and expansion microscopy for fast 3D imaging of virus-infected cells with super-resolution

Expansion microscopy is a sample preparation technique that enables the optical imaging of biological specimens at super-resolution, owing to their physical magnification. Expansion is achieved by embedding the sample in a polymer matrix that swells upon water absorption. The technique makes use of readily available chemicals and does not require sophisticated or custom-made equipment, and therefore offers super-resolution to laboratories that are not specialised in microscopy technologies. The expanded samples are hydrogels that can be imaged with any microscope, as long as the gelled sample can be mounted on that system setup. Here, we focus on the expansion and optical imaging of live attenuated influenza vaccine (LAIV)-infected human cells. We present a protocol to image expanded samples on a light sheet microscope and generate high contrast 3D reconstructions of whole infected cells. The results are superior to those achievable with either widefield or confocal imaging methods for expanded samples and allowed us to visualise structural features of compartments in the infected cells occupied by viral proteins that were not visible before the expansion. In order to promote the optimal combination of expansion and light sheet microscopy, we include a detailed video protocol for the mounting and imaging of gelled samples using a light sheet microscope. The protocol is applicable for super-resolution imaging of virus-host cell interaction in general and we expect that the methodology can greatly contribute to further the research in the field of virology.