PyHIST: A Histological Image Segmentation Tool
Fig 1
(a) The input to the pipeline is a Whole Slide Image (WSI). Within PyHIST, the user can decide to scale down the image to perform the segmentation and tile extraction at lower resolutions. The WSI shown is of a skin tissue sample (GTEX-1117F-0126) from the Genotype-Tissue Expression (GTEx) project [20]. (b) An alternative version of the input image is generated, where the tissue edges are highlighted using a Canny edge detector. A graph segmentation algorithm is employed over this image in order to generate the mask shown in (c). PyHIST extracts tiles of specific dimensions from the masked regions, and provides an overview image to inspect the output of the segmentation and masking procedure, as shown in (d), where the red lines indicate the grid generated by tiling the image at user-specified tile dimensions, while the blue crosses indicate the selected tiles meeting a certain user-specified threshold of tissue content with respect to the total area of the tile. In (e), examples of selected tiles are shown.