Histo-fetch -- On-the-fly processing of gigapixel whole slide images simplifies and speeds neural network training

23 Feb 2021  ·  Brendon Lutnick, Leema Krishna Murali, Brandon Ginley, Avi Z. Rosenberg, Pinaki Sarder ·

We created a custom pipeline (histo-fetch) to efficiently extract random patches and labels from pathology whole slide images (WSIs) for input to a neural network on-the-fly. We prefetch these patches as needed during network training, avoiding the need for WSI preparation such as chopping/tiling. We demonstrate the utility of this pipeline to perform artificial stain transfer and image generation using the popular networks CycleGAN and ProGAN, respectively.

PDF Abstract

Datasets


  Add Datasets introduced or used in this paper

Results from the Paper


  Submit results from this paper to get state-of-the-art GitHub badges and help the community compare results to other papers.

Methods