Journal of Pathology Informatics

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


Brendon Lutnick1, Leema Krishna Murali2, Brandon Ginley1, Avi Z Rosenberg3, Pinaki Sarder4 
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

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.


How to cite this article:
Lutnick B, Murali LK, Ginley B, Rosenberg AZ, Sarder P. Histo-fetch – On-the-fly processing of gigapixel whole slide images simplifies and speeds neural network training.J Pathol Inform 2022;13:7-7


How to cite this URL:
Lutnick B, Murali LK, Ginley B, Rosenberg AZ, Sarder P. Histo-fetch – On-the-fly processing of gigapixel whole slide images simplifies and speeds neural network training. J Pathol Inform [serial online] 2022 [cited 2022 Jan 19 ];13:7-7
Available from: https://www.jpathinformatics.org/article.asp?issn=2153-3539;year=2022;volume=13;issue=1;spage=7;epage=7;aulast=Lutnick;type=0