A computer implemented method for increasing the signal to noise ratio in digital pathology image data to be processed by a digital pathology image analysis algorithm, where one or more processors are programmed to perform steps comprising: receiving an identification of a digital slide image, a classifier associated with a desired characteristic, and a macro comprising a linear or parallel sequence of multiple analysis algorithms; analyzing the digital slide image using the classifier to generate a first metadata mask that defines one or more contiguous regions of the digital slide image data that do not include the desired characteristic; and, for each of the multiple analysis algorithms, applying the first metadata mask to the digital slide image to mask non-desired image data in the digital slide image and obtain first image data from the digital slide image that only includes the desired characteristic, thereby reducing undesirable image data such that the first image data has an improved signal to noise ratio, and processing the obtained first image data using the analysis algorithm to generate a first analysis of the digital slide image, wherein the metadata mask is generated relative to a scanned resolution of the digital slide image, and wherein at least one of the multiple analysis algorithms analyzes image data at a different resolution than the scanned resolution, the method further comprising, for the at least one analysis algorithm, scaling the metadata mask from the scanned resolution to the different resolution, applying the scaled metadata mask to the digital slide image scaled at the different resolution to obtain the first image data at the different resolution, and processing the obtained first image data at the different resolution using the at least one analysis algorithm. receiving an identification of a digital slide image, a classifier associated with a desired characteristic, and a macro comprising a linear or parallel sequence of multiple analysis algorithms; analyzing the digital slide image using the classifier to generate a first metadata mask that defines one or more contiguous regions of the digital slide image data that do not include the desired characteristic; and, for each of the multiple analysis algorithms, applying the first metadata mask to the digital slide image to mask non-desired image data in the digital slide image and obtain first image data from the digital slide image that only includes the desired characteristic, thereby reducing undesirable image data such that the first image data has an improved signal to noise ratio, and processing the obtained first image data using the analysis algorithm to generate a first analysis of the digital slide image, applying the first metadata mask to the digital slide image to mask non-desired image data in the digital slide image and obtain first image data from the digital slide image that only includes the desired characteristic, thereby reducing undesirable image data such that the first image data has an improved signal to noise ratio, and processing the obtained first image data using the analysis algorithm to generate a first analysis of the digital slide image, wherein the metadata mask is generated relative to a scanned resolution of the digital slide image, and wherein at least one of the multiple analysis algorithms analyzes image data at a different resolution than the scanned resolution, the method further comprising, for the at least one analysis algorithm, scaling the metadata mask from the scanned resolution to the different resolution, applying the scaled metadata mask to the digital slide image scaled at the different resolution to obtain the first image data at the different resolution, and processing the obtained first image data at the different resolution using the at least one analysis algorithm.