Journal of Pathology Informatics Journal of Pathology Informatics
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TECHNICAL NOTE
Year : 2022  |  Volume : 13  |  Issue : 1  |  Page : 7

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


1 Department of Pathology and Anatomical Sciences, SUNY Buffalo, Buffalo, New York, USA
2 Department of Biomedical Engineering, SUNY Buffalo, Buffalo, New York, USA
3 Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
4 Department of Pathology and Anatomical Sciences, SUNY Buffalo; Department of Biomedical Engineering, SUNY Buffalo, Buffalo, New York, USA

Correspondence Address:
Prof. Pinaki Sarder
Department of Pathology and Anatomical Sciences, SUNY Buffalo, Buffalo, New York
USA
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Source of Support: None, Conflict of Interest: None


DOI: 10.4103/jpi.jpi_59_20

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Background: Training convolutional neural networks using pathology whole slide images (WSIs) is traditionally prefaced by the extraction of a training dataset of image patches. While effective, for large datasets of WSIs, this dataset preparation is inefficient. Methods: We created a custom pipeline (histo-fetch) to efficiently extract random patches and labels from pathology 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. Results & Conclusions: We demonstrate the utility of this pipeline to perform artificial stain transfer and image generation using the popular networks CycleGAN and ProGAN, respectively. For a large WSI dataset, histo-fetch is 98.6% faster to start training and used 7535x less disk space.


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