# Deep learning-based compression of giga-resolution whole slide images

arXiv: https://arxiv.org/abs/2605.17668 · HTML: https://mlsanity.com/paper/2605.17668/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 18 of its 41 references that are in the map.
- First posted on arXiv 17 May 2026.

## Builds on (most cited first, 18 of 18)

- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Variational image compression with a scale hyperprior](https://mlsanity.com/paper/1802.01436/) (2018)
- [End-to-end Optimized Image Compression](https://mlsanity.com/paper/1611.01704/) (2016)
- [Joint Autoregressive and Hierarchical Priors for Learned Image Compression](https://mlsanity.com/paper/1809.02736/) (2018)
- [Learned Image Compression with Discretized Gaussian Mixture Likelihoods and Attention Modules](https://mlsanity.com/paper/2001.01568/) (2020)
- [High-Fidelity Generative Image Compression](https://mlsanity.com/paper/2006.09965/) (2020)
- [ELIC: Efficient Learned Image Compression with Unevenly Grouped Space-Channel Contextual Adaptive Coding](https://mlsanity.com/paper/2203.10886/) (2022)
- [Lossy Image Compression with Compressive Autoencoders](https://mlsanity.com/paper/1703.00395/) (2017)
- [CompressAI: a PyTorch library and evaluation platform for end-to-end compression research](https://mlsanity.com/paper/2011.03029/) (2020)
- [Real-Time Adaptive Image Compression](https://mlsanity.com/paper/1705.05823/) (2017)
- [Improved Lossy Image Compression with Priming and Spatially Adaptive Bit Rates for Recurrent Networks](https://mlsanity.com/paper/1703.10114/) (2017)
- [Efficient Nonlinear Transforms for Lossy Image Compression](https://mlsanity.com/paper/1802.00847/) (2018)
- [FastPathology: An open-source platform for deep learning-based research and decision support in digital pathology](https://mlsanity.com/paper/2011.06033/) (2020)
- [A Comparative Study of U-Net Topologies for Background Removal in Histopathology Images](https://mlsanity.com/paper/2006.06531/) (2020)
- [Learned Image Compression for HE-stained Histopathological Images via Stain Deconvolution](https://mlsanity.com/paper/2406.12623/) (2024)
- [A Deep Learning-based Compression and Classification Technique for Whole Slide Histopathology Images](https://mlsanity.com/paper/2305.07161/) (2023)
- [Enhanced Diagnostic Fidelity in Pathology Whole Slide Image Compression via Deep Learning](https://mlsanity.com/paper/2503.11350/) (2025)

## Abstract (arXiv)

Implementation of digital pathology leads to an increased number of whole slide images (WSIs). The large size of WSIs is challenging. Today, WSIs are compressed with codecs like JPEG resulting in several gigabytes per WSI, and large amounts of space are wasted storing glass. In this study, deep learning-based tissue segmentation for glass removal, and deep learning compression methods were explored and compared with JPEG, JPEG-2000 and JPEG-XL. Image pyramids (N=21) with intact glass, glass replaced by single-colored pixels, and glass replaced by zero-byte tiles were created and compressed with JPEG, JPEG-XL and a deep learning model. Additionally, several compression models were evaluated on a tissue patch dataset and compared with JPEG, JPEG-2000 and JPEG-XL. Removing glass reduced file sizes considerably for JPEG and JPEG-XL. Deep learning-based image compression reduced the WSI size by 43-72% compared to JPEG compression, whereas deep learning-based glass removal reduced the WSI size by 0.3-33%, and 6-62% using only single-colored pixels and removing all-glass tiles, respectively. Combining the two gave a small improvement to a 44-80% total size reduction which indicates that deep learning-based image compression is able to efficiently compress glass tiles, whereas JPEG is not. On the tissue patch dataset, the best deep learning-based compression models saved on average ~35-40% per patch compared to JPEG, while keeping an average SSIM above 0.95, whereas JPEG-XL and JPEG-2000 saved 17% and 14%, respectively while keeping an SSIM of 0.96. However, the deep learning models had higher decompression times than JPEG and JPEG-XL.