# Data-driven Nucleus Subclassification on Colon H&E using Style-transferred Digital Pathology

arXiv: https://arxiv.org/abs/2407.06116 · HTML: https://mlsanity.com/paper/2407.06116/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 18 of its 33 references that are in the map.
- First posted on arXiv 15 May 2024.

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

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift](https://mlsanity.com/paper/1502.03167/) (2015)
- [Generative Adversarial Networks](https://mlsanity.com/paper/2203.00667/) (2022)
- [Conditional Generative Adversarial Nets](https://mlsanity.com/paper/1411.1784/) (2014)
- [Instance Normalization: The Missing Ingredient for Fast Stylization](https://mlsanity.com/paper/1607.08022/) (2016)
- [HoVer-Net: Simultaneous Segmentation and Classification of Nuclei in Multi-Tissue Histology Images](https://mlsanity.com/paper/1812.06499/) (2018)
- [Gland Segmentation in Colon Histology Images: The GlaS Challenge Contest](https://mlsanity.com/paper/1603.00275/) (2016)
- [Segment Anything Model (SAM) for Digital Pathology: Assess Zero-shot Segmentation on Whole Slide Imaging](https://mlsanity.com/paper/2304.04155/) (2023)
- [PanNuke Dataset Extension, Insights and Baselines](https://mlsanity.com/paper/2003.10778/) (2020)
- [Lizard: A Large-Scale Dataset for Colonic Nuclear Instance Segmentation and Classification](https://mlsanity.com/paper/2108.11195/) (2021)
- [MILD-Net: Minimal Information Loss Dilated Network for Gland Instance Segmentation in Colon Histology Images](https://mlsanity.com/paper/1806.01963/) (2018)
- [CoNIC: Colon Nuclei Identification and Counting Challenge 2022](https://mlsanity.com/paper/2111.14485/) (2021)
- [Deep Learning-enabled Virtual Histological Staining of Biological Samples](https://mlsanity.com/paper/2211.06822/) (2022)
- [All-in-SAM: from Weak Annotation to Pixel-wise Nuclei Segmentation with Prompt-based Finetuning](https://mlsanity.com/paper/2307.00290/) (2023)
- [Digital synthesis of histological stains using micro-structured and multiplexed virtual staining of label-free tissue](https://mlsanity.com/paper/2001.07267/) (2020)
- [Cell Spatial Analysis in Crohn's Disease: Unveiling Local Cell Arrangement Pattern with Graph-based Signatures](https://mlsanity.com/paper/2308.10166/) (2023)
- [Nucleus subtype classification using inter-modality learning](https://mlsanity.com/paper/2401.05602/) (2024)

## Abstract (arXiv)

Understanding the way cells communicate, co-locate, and interrelate is essential to furthering our understanding of how the body functions. H&E is widely available, however, cell subtyping often requires expert knowledge and the use of specialized stains. To reduce the annotation burden, AI has been proposed for the classification of cells on H&E. For example, the recent Colon Nucleus Identification and Classification (CoNIC) Challenge focused on labeling 6 cell types on H&E of the colon. However, the CoNIC Challenge was unable to classify epithelial subtypes (progenitor, enteroendocrine, goblet), lymphocyte subtypes (B, helper T, cytotoxic T), and connective subtypes (fibroblasts). We use inter-modality learning to label previously un-labelable cell types on H&E. We take advantage of multiplexed immunofluorescence (MxIF) histology to label 14 cell subclasses. We performed style transfer on the same MxIF tissues to synthesize realistic virtual H&E which we paired with the MxIF-derived cell subclassification labels. We evaluated the efficacy of using a supervised learning scheme where the input was realistic-quality virtual H&E and the labels were MxIF-derived cell subclasses. We assessed our model on private virtual H&E and public real H&E. On virtual H&E, we were able to classify helper T cells and epithelial progenitors with positive predictive values of 0.34 ± 0.15 (prevalence 0.03 ± 0.01) and 0.47 ± 0.1 (prevalence 0.07 ± 0.02) respectively, when using ground truth centroid information. On real H&E we could classify helper T cells and epithelial progenitors with upper bound positive predictive values of 0.43 ± 0.03 (parent class prevalence 0.21) and 0.94 ± 0.02 (parent class prevalence 0.49) when using ground truth centroid information. This is the first work to provide cell type classification for helper T and epithelial progenitor nuclei on H&E.