Our method directly generates key features based on the whole image without requiring a region selection step. Using the key features and cell-level information found by the deep neural networks, we automatically annotated whole-mount pathology images. Here we show an automatically annotated whole-mount pathology image (left), as well as a low-magnification image of the yellow region (upper right) and the associated high-magnification images with number of Step 2 feature (lower right). The regions with impact scores above and below 0.5 in Step 1 are shaded in red and blue, respectively. The indicated yellow cell shows [number of Step 1 feature (100 total features)] [impact score, Step 1] [impact score, Step 2] (see Key feature generation method in the Methods section). The black scale bar included in the image represents a length of 1 cm. The green scale bar represents a length of 100 μm. The blue scale bar represents a length of 12.3 μm.