A technical system for determining the slide quality of a digital microscope slide, the system comprising: a computer readable storage medium for storing computer executable programmed modules; a processor communicatively coupled with the computer readable storage medium for executing programmed modules stored therein; a micro-analysis module stored in the computer readable storage medium and configured to divide the digital microscope slide image into a plurality of blocks of nxn block size, determine, for each of one or more of said plurality of blocks whether it should be qualified for determining slide quality, wherein a block is qualified if it does not contain an amount of white space above a first threshold and its brightness is not below a second threshold or above a third threshold, analyze each of the qualified one or more blocks with a plurality of partial frequency transforms to generate a block frequency transform for each qualified block, wherein each partial frequency transform is a frequency transform for a respective part of the block, generate a quality score for each qualified block based on the block frequency transform corresponding to that qualified block by summing the results of the partial frequency transforms, wherein the sum is weighted over the spatial frequencies, and generate a markup image by blending each qualified block's original image converted to gray scale with a block of color related to the quality score for the qualified block; and a macro-analysis module stored in the computer readable storage medium and configured to combine the quality scores into a score map which represents each block's quality score with dimensions of the digital microscope slide image scaled by the block size, detect artifacts by identifying score discontinuity trends along horizontal or vertical dimensions in the score map, and compute a whole slide score in accordance with the combined quality scores and detected artifacts by computing an average of the quality scores minus an artifact degradation score for each detected artifact. a computer readable storage medium for storing computer executable programmed modules; a processor communicatively coupled with the computer readable storage medium for executing programmed modules stored therein; a micro-analysis module stored in the computer readable storage medium and configured to divide the digital microscope slide image into a plurality of blocks of nxn block size, determine, for each of one or more of said plurality of blocks whether it should be qualified for determining slide quality, wherein a block is qualified if it does not contain an amount of white space above a first threshold and its brightness is not below a second threshold or above a third threshold, analyze each of the qualified one or more blocks with a plurality of partial frequency transforms to generate a block frequency transform for each qualified block, wherein each partial frequency transform is a frequency transform for a respective part of the block, generate a quality score for each qualified block based on the block frequency transform corresponding to that qualified block by summing the results of the partial frequency transforms, wherein the sum is weighted over the spatial frequencies, and generate a markup image by blending each qualified block's original image converted to gray scale with a block of color related to the quality score for the qualified block; and divide the digital microscope slide image into a plurality of blocks of nxn block size, determine, for each of one or more of said plurality of blocks whether it should be qualified for determining slide quality, wherein a block is qualified if it does not contain an amount of white space above a first threshold and its brightness is not below a second threshold or above a third threshold, analyze each of the qualified one or more blocks with a plurality of partial frequency transforms to generate a block frequency transform for each qualified block, wherein each partial frequency transform is a frequency transform for a respective part of the block, generate a quality score for each qualified block based on the block frequency transform corresponding to that qualified block by summing the results of the partial frequency transforms, wherein the sum is weighted over the spatial frequencies, and generate a markup image by blending each qualified block's original image converted to gray scale with a block of color related to the quality score for the qualified block; and a macro-analysis module stored in the computer readable storage medium and configured to combine the quality scores into a score map which represents each block's quality score with dimensions of the digital microscope slide image scaled by the block size, detect artifacts by identifying score discontinuity trends along horizontal or vertical dimensions in the score map, and compute a whole slide score in accordance with the combined quality scores and detected artifacts by computing an average of the quality scores minus an artifact degradation score for each detected artifact. combine the quality scores into a score map which represents each block's quality score with dimensions of the digital microscope slide image scaled by the block size, detect artifacts by identifying score discontinuity trends along horizontal or vertical dimensions in the score map, and compute a whole slide score in accordance with the combined quality scores and detected artifacts by computing an average of the quality scores minus an artifact degradation score for each detected artifact.