A method for operating a microscope scanner, the method comprising: generating pre-scan data for a target comprising a sample, wherein generating the pre-scan data comprises: obtaining a pre-scan image of the target from a pre-scan; and identifying one or more sample-containing regions and one or more sample-free regions of the target from the pre-scan image, wherein the one or more sample-containing regions correspond to locations on the target in which the sample is expected to be present and wherein the one or more sample-free regions correspond to locations on the target where the sample is expected to be absent; and performing an imaging scan of a scanning region of the target, the scanning region including the one or more sample-containing regions and the one or more sample-free regions, characterised in that the microscope scanner comprises a line scanner, wherein performing the imaging scan comprises: moving the line scanner relative to the target along an image scan path and acquiring an image of the target at each of a plurality of locations along the image scan path using the line scanner; adjusting the scanning speed of the line scanner along the image scan path based on the pre-scan data so that the target is imaged at a higher scanning speed within the one or more sample-free regions than in the one or more sample-containing regions; monitoring one or more image parameters from the images of the target acquired along the image scan path; and further adjusting the scanning speed of the line scanner within the one or more sample-free regions in response to a change in said one or more image parameters; wherein the one or more image parameters comprise a focus merit value, and wherein the scanning speed of the line scanner is decreased in response to the focus merit value increasing. generating pre-scan data for a target comprising a sample, wherein generating the pre-scan data comprises: obtaining a pre-scan image of the target from a pre-scan; and identifying one or more sample-containing regions and one or more sample-free regions of the target from the pre-scan image, wherein the one or more sample-containing regions correspond to locations on the target in which the sample is expected to be present and wherein the one or more sample-free regions correspond to locations on the target where the sample is expected to be absent; and obtaining a pre-scan image of the target from a pre-scan; and identifying one or more sample-containing regions and one or more sample-free regions of the target from the pre-scan image, wherein the one or more sample-containing regions correspond to locations on the target in which the sample is expected to be present and wherein the one or more sample-free regions correspond to locations on the target where the sample is expected to be absent; and performing an imaging scan of a scanning region of the target, the scanning region including the one or more sample-containing regions and the one or more sample-free regions, characterised in that the microscope scanner comprises a line scanner, wherein performing the imaging scan comprises: moving the line scanner relative to the target along an image scan path and acquiring an image of the target at each of a plurality of locations along the image scan path using the line scanner; adjusting the scanning speed of the line scanner along the image scan path based on the pre-scan data so that the target is imaged at a higher scanning speed within the one or more sample-free regions than in the one or more sample-containing regions; monitoring one or more image parameters from the images of the target acquired along the image scan path; and further adjusting the scanning speed of the line scanner within the one or more sample-free regions in response to a change in said one or more image parameters; wherein the one or more image parameters comprise a focus merit value, and wherein the scanning speed of the line scanner is decreased in response to the focus merit value increasing. moving the line scanner relative to the target along an image scan path and acquiring an image of the target at each of a plurality of locations along the image scan path using the line scanner; adjusting the scanning speed of the line scanner along the image scan path based on the pre-scan data so that the target is imaged at a higher scanning speed within the one or more sample-free regions than in the one or more sample-containing regions; monitoring one or more image parameters from the images of the target acquired along the image scan path; and further adjusting the scanning speed of the line scanner within the one or more sample-free regions in response to a change in said one or more image parameters; wherein the one or more image parameters comprise a focus merit value, and wherein the scanning speed of the line scanner is decreased in response to the focus merit value increasing.