A handheld diagnostic system may include a disposable sample holder for receiving and containing a biological sample and an analysis module having a chip-scale microscope. The sample holder may include a plurality of uniformly spaced tick marks. The analysis module may include a sensor for detecting the tick marks as the sample holder is inserted into the analysis module. The chip-scale microscope may include an image sensor for capturing images of the sample. Each time the sensor detects a tick mark, control circuitry may issue a control signal to the image sensor to capture an image of the biological sample. This type of automated image capture mechanism ensures that images are captured at a uniform spatial distribution even when the sample holder is inserted into the analysis module at variable speed. The analysis module may transmit sample imaging data to a portable electronic device.