# A Multi-Stage Auto-Context Deep Learning Framework for Tissue and Nuclei Segmentation and Classification in H&E-Stained Histological Images of Advanced Melanoma

arXiv: https://arxiv.org/abs/2503.23958 · HTML: https://mlsanity.com/paper/2503.23958/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 27 of its 60 references that are in the map.
- First posted on arXiv 31 Mar 2025.

## Builds on (most cited first, 27 of 27)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Very Deep Convolutional Networks for Large-Scale Image Recognition](https://mlsanity.com/paper/1409.1556/) (2014)
- [ImageNet Large Scale Visual Recognition Challenge](https://mlsanity.com/paper/1409.0575/) (2014)
- [Mask R-CNN](https://mlsanity.com/paper/1703.06870/) (2017)
- [Grad-CAM: Visual Explanations from Deep Networks via Gradient-based Localization](https://mlsanity.com/paper/1610.02391/) (2016)
- [SegFormer: Simple and Efficient Design for Semantic Segmentation with Transformers](https://mlsanity.com/paper/2105.15203/) (2021)
- [Rethinking Atrous Convolution for Semantic Image Segmentation](https://mlsanity.com/paper/1706.05587/) (2017)
- [UNet++: A Nested U-Net Architecture for Medical Image Segmentation](https://mlsanity.com/paper/1807.10165/) (2018)
- [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)
- [BACH: Grand Challenge on Breast Cancer Histology Images](https://mlsanity.com/paper/1808.04277/) (2018)
- [CellViT: Vision Transformers for Precise Cell Segmentation and Classification](https://mlsanity.com/paper/2306.15350/) (2023)
- [Deep learning-based transformation of the H&E stain into special stains](https://mlsanity.com/paper/2008.08871/) (2020)
- [CryoNuSeg: A Dataset for Nuclei Instance Segmentation of Cryosectioned H&E-Stained Histological Images](https://mlsanity.com/paper/2101.00442/) (2021)
- [NuClick: A Deep Learning Framework for Interactive Segmentation of Microscopy Images](https://mlsanity.com/paper/2005.14511/) (2020)
- [HookNet: multi-resolution convolutional neural networks for semantic segmentation in histopathology whole-slide images](https://mlsanity.com/paper/2006.12230/) (2020)
- [One Model is All You Need: Multi-Task Learning Enables Simultaneous Histology Image Segmentation and Classification](https://mlsanity.com/paper/2203.00077/) (2022)
- [Towards Label-efficient Automatic Diagnosis and Analysis: A Comprehensive Survey of Advanced Deep Learning-based Weakly-supervised, Semi-supervised and Self-supervised Techniques in Histopathological Image Analysis](https://mlsanity.com/paper/2208.08789/) (2022)
- [OCELOT: Overlapped Cell on Tissue Dataset for Histopathology](https://mlsanity.com/paper/2303.13110/) (2023)
- [NuInsSeg: A Fully Annotated Dataset for Nuclei Instance Segmentation in H&E-Stained Histological Images](https://mlsanity.com/paper/2308.01760/) (2023)
- [A Tour of Unsupervised Deep Learning for Medical Image Analysis](https://mlsanity.com/paper/1812.07715/) (2018)
- [Investigating and Exploiting Image Resolution for Transfer Learning-based Skin Lesion Classification](https://mlsanity.com/paper/2006.14715/) (2020)
- [Deep Neural Network Pruning for Nuclei Instance Segmentation in Hematoxylin & Eosin-Stained Histological Images](https://mlsanity.com/paper/2206.07422/) (2022)
- [Towards Effective and Efficient Context-aware Nucleus Detection in Histopathology Whole Slide Images](https://mlsanity.com/paper/2503.05678/) (2025)
- [SoftCTM: Cell detection by soft instance segmentation and consideration of cell-tissue interaction](https://mlsanity.com/paper/2312.12151/) (2023)
- [Evaluating Pre-trained Convolutional Neural Networks and Foundation Models as Feature Extractors for Content-based Medical Image Retrieval](https://mlsanity.com/paper/2409.09430/) (2024)
- [Nuclei & Glands Instance Segmentation in Histology Images: A Narrative Review](https://mlsanity.com/paper/2208.12460/) (2022)

## Built on by (most cited first, 4 of 4)

- [ACS-SegNet: An Attention-Based CNN-SegFormer Segmentation Network for Tissue Segmentation in Histopathology](https://mlsanity.com/paper/2510.20754/) (2025)
- [NucFuseRank: Dataset Fusion and Performance Ranking for Nuclei Instance Segmentation](https://mlsanity.com/paper/2601.20104/) (2026)
- [Hard Vision, Easy Vision: What GPT-6 Astra Reveals Across Computer Vision](https://mlsanity.com/paper/2609.35718/) (2026)
- [Fusion of Foundation and Vision Transformer Model Features for Dermatoscopic Image Classification](https://mlsanity.com/paper/2505.16338/) (2025)

## Abstract (arXiv)

Melanoma is the most lethal form of skin cancer, with an increasing incidence rate worldwide. Analyzing histological images of melanoma by localizing and classifying tissues and cell nuclei is considered the gold standard method for diagnosis and treatment options for patients. While many computerized approaches have been proposed for automatic analysis, most perform tissue-based analysis and nuclei (cell)-based analysis as separate tasks, which might be suboptimal. In this work, using the PUMA challenge dataset, we propose a novel multi-stage deep learning approach by combining tissue and nuclei information in a unified framework based on the auto-context concept to perform segmentation and classification in histological images of melanoma. Through pre-training and further post-processing, our approach achieved second and first place rankings in the PUMA challenge, with average micro Dice tissue score and summed nuclei F1-score of 73.40% for Track 1 and 63.48% for Track 2, respectively. Furthermore, through a comprehensive ablation study and additional evaluation on an external dataset, we demonstrated the effectiveness of the framework components as well as the generalization capabilities of the proposed approach. Our implementation for training and testing is available at: https://github.com/NimaTorbati/PumaSubmit