A method for operating a microscope scanner comprising a detector array, the method comprising: performing a pre-scan so as to generate a pre-scan image of a target, wherein the target comprises a sample, and wherein the depth of focus for the pre-scan is in excess of 500 micrometres; performing an automated image analysis of the pre-scan image to produce a first probability map indicating where the sample is expected to be present on the target; performing a first imaging scan of one or more area(s) of interest, AOI, on the target, wherein the one or more AOI are selected from the first probability map, and wherein performing the first imaging scan comprises: moving the detector array 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 detector array, wherein the depth of focus for each image acquired during the first imaging scan is below 3 micrometres; generating focus control data during the imaging scan, wherein generating focus control data comprises calculating a focus merit value at each said location along the image scan path; and adjusting the focal height of the detector array along the image scan path based on said focus merit values; analysing the efficacy of the first imaging scan using the focus control data and determining a change to one or more scanning parameters from the first imaging scan, for the performance of a second imaging scan, based on this analysis. performing a pre-scan so as to generate a pre-scan image of a target, wherein the target comprises a sample, and wherein the depth of focus for the pre-scan is in excess of 500 micrometres; performing an automated image analysis of the pre-scan image to produce a first probability map indicating where the sample is expected to be present on the target; performing a first imaging scan of one or more area(s) of interest, AOI, on the target, wherein the one or more AOI are selected from the first probability map, and wherein performing the first imaging scan comprises: moving the detector array 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 detector array, wherein the depth of focus for each image acquired during the first imaging scan is below 3 micrometres; generating focus control data during the imaging scan, wherein generating focus control data comprises calculating a focus merit value at each said location along the image scan path; and adjusting the focal height of the detector array along the image scan path based on said focus merit values; moving the detector array 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 detector array, wherein the depth of focus for each image acquired during the first imaging scan is below 3 micrometres; generating focus control data during the imaging scan, wherein generating focus control data comprises calculating a focus merit value at each said location along the image scan path; and adjusting the focal height of the detector array along the image scan path based on said focus merit values; analysing the efficacy of the first imaging scan using the focus control data and determining a change to one or more scanning parameters from the first imaging scan, for the performance of a second imaging scan, based on this analysis.