A method in a linear-array-based microscope slide scanner, the method comprising: scanning a microscope slide to acquire image data in the form of a plurality of overlapping image stripes, wherein acquiring each of the plurality of overlapping image stripes comprises either establishing a line-scan buffer, receiving position feedback information from a position encoder, and using a strobe light to saturate a linear-array detector of the microscope slide scanner for lines of data of the line-scan buffer that correspond to a starting point of valid line-scan data, or receiving position feedback information from a position encoder, initiating data capture using an output of the position encoder to initiate an external trigger after a coarse alignment synchronization flag has been set, and turning off the data capture when a desired number of lines of data comprising valid line-scan data have been captured; while scanning, combining the plurality of overlapping image stripes into a baseline image by aligning each pair of adjacent image stripes (70, 72) by calculating an offset between the adjacent image stripes by pattern matching within an overlap region between the adjacent image stripes (70, 72), and compressing the image data to eliminate storage of uncompressed image stripes in persistent memory; organizing the baseline image into a plurality of image tiles (114, 260); and storing the tiled baseline image in a data storage area. scanning a microscope slide to acquire image data in the form of a plurality of overlapping image stripes, wherein acquiring each of the plurality of overlapping image stripes comprises either establishing a line-scan buffer, receiving position feedback information from a position encoder, and using a strobe light to saturate a linear-array detector of the microscope slide scanner for lines of data of the line-scan buffer that correspond to a starting point of valid line-scan data, or receiving position feedback information from a position encoder, initiating data capture using an output of the position encoder to initiate an external trigger after a coarse alignment synchronization flag has been set, and turning off the data capture when a desired number of lines of data comprising valid line-scan data have been captured; establishing a line-scan buffer, receiving position feedback information from a position encoder, and using a strobe light to saturate a linear-array detector of the microscope slide scanner for lines of data of the line-scan buffer that correspond to a starting point of valid line-scan data, or receiving position feedback information from a position encoder, initiating data capture using an output of the position encoder to initiate an external trigger after a coarse alignment synchronization flag has been set, and turning off the data capture when a desired number of lines of data comprising valid line-scan data have been captured; while scanning, combining the plurality of overlapping image stripes into a baseline image by aligning each pair of adjacent image stripes (70, 72) by calculating an offset between the adjacent image stripes by pattern matching within an overlap region between the adjacent image stripes (70, 72), and compressing the image data to eliminate storage of uncompressed image stripes in persistent memory; combining the plurality of overlapping image stripes into a baseline image by aligning each pair of adjacent image stripes (70, 72) by calculating an offset between the adjacent image stripes by pattern matching within an overlap region between the adjacent image stripes (70, 72), and compressing the image data to eliminate storage of uncompressed image stripes in persistent memory; organizing the baseline image into a plurality of image tiles (114, 260); and storing the tiled baseline image in a data storage area.