Provided are automated (computerized) methods and systems for analyzing digitized pathology images in a variety of tissues potentially containing diseased or neoplastic cells. The method utilizes a coarse-to-fine analysis, in which an entire image is tiled and shape, color, and texture features are extracted in each tile, as primary features. A representative subset of tiles is determined within a cluster of similar tiles. A statistical analysis (e.g. principal component analysis) reduces the substantial number of “coarse” features, decreasing computational complexity of the classification algorithm. Afterwards, a fine stage provides a detailed analysis of a single representative tile from each group. A second statistical step uses a regression algorithm (e.g. elastic net classifier) to produce a diagnostic decision value for each representative tile. A weighted voting scheme aggregates the decision values from these tiles to obtain a diagnosis at the whole slide level.