A stuck slide determination system is provided that determines if a slide (e.g., glass slide), positioned on a scanning stage at the start of the scanning process, gets stuck and does not move along with the scanning stage after the scanning process commences. In an embodiment, the system includes a sensor having a transmitter and receiver that are relatively positioned to detect the presence of the stage or a slide or the absence of the stage or a slide. When the scanning stage begins to move at the start of the scanning process, a processor monitors a signal from the sensor and determines if the slide is improperly positioned after the scanning process has commenced. If the slide is improperly positioned, the processor stops movement of the scanning stage in order to protect the slide from damage.