Figure 1.

Overview of virtual IF staining with SHIFT and feature-guided H&E sample selection. (a) Schematic of SHIFT modeling for training and testing phases. The generator network $G$ generates virtual IF tiles conditioned on H&E tiles. The discriminator network $D$ learns to discriminate between real and generated image pairs. See also Supplementary Fig. S2. (b) Four heterogeneous samples of H&E-stained PDAC biopsy tissue used in the current study. Pathologist annotations indicate regions that are benign (green), grade 1 PDAC (black), grade 2/3 PDAC (blue), and grade 2/3 adenosquamous (red). (c) Making direct comparisons between H&E whole slide images (WSIs) is intractable because each WSI can contain billions of pixels. By decomposing WSIs into sets of non-overlapping 256 × 256 pixel tiles, we can make tractable comparisons between the feature-wise distribution of tile sets. (d) Schematic of feature-guided H&E sample selection. First, H&E samples are decomposed into 256 × 256 pixel tiles. Second, all H&E tiles are used to train a variational autoencoder (VAE) to learn feature representations for all tiles; for each 196,608-pixel H&E tile in the dataset, the encoder $\mathcal{E}$ learns a compact but expressive feature representation that maximizes the ability of the decoder $\mathcal{D}$ to reconstruct the original tile from its feature representation (see “Methods”). Third, the tile feature representations are used to determine which samples are most representative of the whole dataset.