A method comprising using at least one hardware processor of a scanning system to: initialize a focus map; add focus points to the focus map while acquiring a plurality of image stripes of at least a portion of a sample on a glass slide, by, for each of the plurality of image stripes, acquiring each of a plurality of frames, collectively representing the image stripe using both an imaging line-scan camera and a tilted focusing line-scan camera, and adding focus points, representing positions of best focus for trusted ones of the plurality of frames, to the focus map; determine whether or not to restripe one or more of the plurality of image stripes based on a focus error for each of the plurality of frames in the plurality of image stripes; when determining to restripe one or more image stripes, reacquire the one or more image stripes; and assemble the plurality of image stripes into a composite image of the at least a portion of the sample characterized in that: fl any outlying focus points are removed from the focus map; and the plurality of image stripes are acquired by, in order: acquiring a reference stripe; acquiring image stripes, in sequence, from a first side of the reference stripe to a first edge of a scan area of the sample; and acquiring image stripes, in sequence, from a second side of the reference stripe, which is opposite the first side of the reference stripe, to a second edge of the scan area, which is opposite the first edge of the scan area. initialize a focus map; add focus points to the focus map while acquiring a plurality of image stripes of at least a portion of a sample on a glass slide, by, for each of the plurality of image stripes, acquiring each of a plurality of frames, collectively representing the image stripe using both an imaging line-scan camera and a tilted focusing line-scan camera, and adding focus points, representing positions of best focus for trusted ones of the plurality of frames, to the focus map; acquiring each of a plurality of frames, collectively representing the image stripe using both an imaging line-scan camera and a tilted focusing line-scan camera, and adding focus points, representing positions of best focus for trusted ones of the plurality of frames, to the focus map; determine whether or not to restripe one or more of the plurality of image stripes based on a focus error for each of the plurality of frames in the plurality of image stripes; when determining to restripe one or more image stripes, reacquire the one or more image stripes; and assemble the plurality of image stripes into a composite image of the at least a portion of the sample characterized in that: fl any outlying focus points are removed from the focus map; and the plurality of image stripes are acquired by, in order: acquiring a reference stripe; acquiring image stripes, in sequence, from a first side of the reference stripe to a first edge of a scan area of the sample; and acquiring image stripes, in sequence, from a second side of the reference stripe, which is opposite the first side of the reference stripe, to a second edge of the scan area, which is opposite the first edge of the scan area. acquiring a reference stripe; acquiring image stripes, in sequence, from a first side of the reference stripe to a first edge of a scan area of the sample; and acquiring image stripes, in sequence, from a second side of the reference stripe, which is opposite the first side of the reference stripe, to a second edge of the scan area, which is opposite the first edge of the scan area.