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

Brendon Lutnick; Leema Krishna Murali; Brandon Ginley; Avi Z. Rosenberg; Pinaki Sarder

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arXiv · 2102.11433

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

Brendon Lutnick·Leema Krishna Murali·Brandon Ginley·Avi Z. Rosenberg·Pinaki Sarder

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Abstract

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.

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Brendon Lutnick, Leema Krishna Murali, Brandon Ginley, Avi Z. Rosenberg, Pinaki Sarder. 2021-02-23. Histo-fetch -- On-the-fly processing of gigapixel whole slide images simplifies and speeds neural network training. https://arxiv.org/abs/2102.11433

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