A rapid and automatic virus imaging and analysis system includes (i) electron optical sub-systems (EOSs), each of which has a large field of view (FOV) and is capable of instant magnification switching for rapidly scanning a virus sample; (ii) sample management sub-systems (SMSs), each of which automatically loads virus samples into one of the EOSs for virus sample scanning and then unloads the virus samples from the EOS after the virus sample scanning is completed; (iii) virus detection and classification sub-systems (VDCSs), each of which automatically detects and classifies a virus based on images from the EOS virus sample scanning; and (iv) a cloud-based collaboration sub-system for analyzing the virus sample scanning images, storing images from the EOS virus sample scanning, and storing and analyzing machine data associated with the EOSs, the SMSs, and the VDCSs.