# DeeperHistReg: Robust Whole Slide Images Registration Framework

arXiv: https://arxiv.org/abs/2404.14434 · HTML: https://mlsanity.com/paper/2404.14434/

## Key facts

- Cited by 6 papers in the map (data through 14 Oct 2026).
- Builds on 5 of its 14 references that are in the map.
- First posted on arXiv 19 Apr 2024.

## Builds on (most cited first, 5 of 5)

- [Comparison of Consecutive and Re-stained Sections for Image Registration in Histopathology](https://mlsanity.com/paper/2106.13150/) (2021)
- [The ACROBAT 2022 Challenge: Automatic Registration Of Breast Cancer Tissue](https://mlsanity.com/paper/2305.18033/) (2023)
- [ACROBAT -- a multi-stain breast cancer histological whole-slide-image data set from routine diagnostics for computational pathology](https://mlsanity.com/paper/2211.13621/) (2022)
- [Deep Feature based Cross-slide Registration](https://mlsanity.com/paper/2202.09971/) (2022)
- [Whole slide image registration for the study of tumor heterogeneity](https://mlsanity.com/paper/1901.08317/) (2019)

## Built on by (most cited first, 6 of 6)

- [GANs vs. Diffusion Models for virtual staining with the HER2match dataset](https://mlsanity.com/paper/2506.18484/) (2025)
- [ZeroReg3D: A Zero-shot Registration Pipeline for 3D Consecutive Histopathology Image Reconstruction](https://mlsanity.com/paper/2506.21923/) (2025)
- [A Scalable Distributed Framework for Multimodal GigaVoxel Image Registration](https://mlsanity.com/paper/2509.25044/) (2025)
- [Automatic Registration of SHG and H&E Images with Feature-based Initial Alignment and Intensity-based Instance Optimization: Contribution to the COMULIS Challenge](https://mlsanity.com/paper/2409.15931/) (2024)
- [INSIGHT: Spatially resolved survival modelling from routine histology crosslinked with molecular profiling reveals prognostic epithelial-immune axes in stage II/III colorectal cancer](https://mlsanity.com/paper/2512.22262/) (2025)
- [PAINT: Pathology-Aware Integrated Next-Scale Transformation for Virtual Immunohistochemistry](https://mlsanity.com/paper/2601.16024/) (2026)

## Abstract (arXiv)

DeeperHistReg is a software framework dedicated to registering whole slide images (WSIs) acquired using multiple stains. It allows one to perform the preprocessing, initial alignment, and nonrigid registration of WSIs acquired using multiple stains (e.g. hematoxylin & eosin, immunochemistry). The framework implements several state-of-the-art registration algorithms and provides an interface to operate on arbitrary resolution of the WSIs (up to 200k x 200k). The framework is extensible and new algorithms can be easily integrated by other researchers. The framework is available both as a PyPI package and as a Docker container.