The present disclosure provides systems and methods for analyzing a plurality of samples of small objects. In various other embodiments, the system includes a staging console for supporting a plurality of sample trays. The system additionally includes a plurality of workstations that each includes a robotic container transfer subsystem for sequentially removing and replacing each of a plurality of sample containers arrayed in the sample trays, each sample container containing a sample of small objects. Each workstation additionally includes an automated analysis subsystem for sequentially receiving each container from the transfer subsystem, removing each sample from the respective container, acquiring data of each sample and returning each sample to the respective container. The system further includes a tray shuttle robot that distributes and retrieves the sample trays to and from the workstations.