Determining angular orientation for imaging

A rotary imaging system for imaging a sample, the system comprising:

• a rotary junction that during operation generates a plurality of image frames of the sample and angular rotational position signals, wherein each angular rotational position signal corresponds to an image frame within a plurality of the image frames and each rotational position signal is generated based on a known position of the rotary junction such that acquisition of each image frame is synchronized to the corresponding known position of the rotary junction;
• an optical engine coupled to the rotary junction to receive the image frames acquired using the rotary junction of the rotary imaging system;
• a data acquisition system coupled to the rotary junction to receive the rotational position signals and align an orientation of the image frames based on the angular rotational position signals, wherein synchronizing acquisition comprises synchronizing acquisition of a first one of the plurality of image frames with a first one of the rotational position signals and synchronizing acquisition of a second one of the plurality of image frames with a second one of the rotational position signals.