Fully automatic rapid microscope slide scanner

A method for creating a contiguous digital image of a portion of a microscope sample, comprising:

• focusing a line scan camera on a plurality of focus points within a microscope sample;
• creating a focus map comprising the plurality of focus points;
• moving a microscope sample at substantially constant velocity relative to the line scan camera having a linear field of view, wherein a first strip of the microscope sample is exposed to the field of view of the line scan camera during said motion;
• illuminating a portion of the first strip while the microscope sample is in motion;
• scanning the first strip with the line scan camera while the sample is in motion;
• adjusting the focus of the line scan camera during said scanning in accordance with the focus map;
• storing a digital image of the first strip;
• moving a microscope sample at substantially constant velocity relative to the line scan camera, wherein a substantially unscanned second strip of the microscope sample is exposed to the field of view of the line scan camera during said motion;
• illuminating a portion of the second strip while the microscope sample is in motion;
• scanning the second strip with the line scan camera while the sample is in motion;
• adjusting the focus of the line scan camera during said scanning;
• storing a digital image of the second strip;
• and
• composing the digital image of the first strip and the digital image of the second strip into a contiguous digital image.