Auto focus system with a mask

An auto-focus system, comprising:

• an illumination path that is configured to illuminate a sample with illumination beams that form multiple spot arrays on the sample that comprises a first set of spot arrays formed on a first side of an imaging area, and a downstream set of spot arrays formed on another side of the imaging area;
• a controller;
• a collection path that is configured to receive first collected beams and second collected beams from the sample;
• wherein the collection path comprises:
• a mask that is located at an entrance pupil, the mask comprises a pair of off-axis slits for truncating each collected beam to provide a pair of rays per each collected beam;
• a beam splitter that is configured to (i) direct to a first branch, first rays associated with the first collected beams, and (ii) direct to an second branch, rays associated with the second collected beams;
• and
• a sensor that follows the first branch and the second branch and is configured to receive a pair of spots per each one of the multiple spot arrays, wherein a distance between spots of each pair is indicative of a focus state associated with a corresponding spot array;
• wherein an optical axis of the first branch is oriented to an optical axis of the second branch.