# Lizard: A Large-Scale Dataset for Colonic Nuclear Instance Segmentation and Classification

arXiv: https://arxiv.org/abs/2108.11195 · HTML: https://mlsanity.com/paper/2108.11195/

## Key facts

- Cited by 89 papers in the map (data through 14 Oct 2026).
- Builds on 15 of its 39 references that are in the map.
- First posted on arXiv 25 Aug 2021.

## Builds on (most cited first, 15 of 15)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Panoptic Segmentation](https://mlsanity.com/paper/1801.00868/) (2018)
- [Explaining Explanations: An Overview of Interpretability of Machine Learning](https://mlsanity.com/paper/1806.00069/) (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)
- [PanNuke Dataset Extension, Insights and Baselines](https://mlsanity.com/paper/2003.10778/) (2020)
- [MILD-Net: Minimal Information Loss Dilated Network for Gland Instance Segmentation in Colon Histology Images](https://mlsanity.com/paper/1806.01963/) (2018)
- [Methods for Segmentation and Classification of Digital Microscopy Tissue Images](https://mlsanity.com/paper/1810.13230/) (2018)
- [Automated Gleason Grading of Prostate Biopsies using Deep Learning](https://mlsanity.com/paper/1907.07980/) (2019)
- [Micro-Net: A unified model for segmentation of various objects in microscopy images](https://mlsanity.com/paper/1804.08145/) (2018)
- [Context-Aware Convolutional Neural Network for Grading of Colorectal Cancer Histology Images](https://mlsanity.com/paper/1907.09478/) (2019)
- [Quantifying Explainers of Graph Neural Networks in Computational Pathology](https://mlsanity.com/paper/2011.12646/) (2020)
- [Towards the Augmented Pathologist: Challenges of Explainable-AI in Digital Pathology](https://mlsanity.com/paper/1712.06657/) (2017)
- [Multi-Task Learning in Histo-pathology for Widely Generalizable Model](https://mlsanity.com/paper/2005.08645/) (2020)

## Built on by (most cited first, 30 of 89)

- [CoNIC: Colon Nuclei Identification and Counting Challenge 2022](https://mlsanity.com/paper/2111.14485/) (2021)
- [Overcoming Data Scarcity in Biomedical Imaging with a Foundational Multi-Task Model](https://mlsanity.com/paper/2311.09847/) (2023)
- [One Model is All You Need: Multi-Task Learning Enables Simultaneous Histology Image Segmentation and Classification](https://mlsanity.com/paper/2203.00077/) (2022)
- [CoNIC Challenge: Pushing the Frontiers of Nuclear Detection, Segmentation, Classification and Counting](https://mlsanity.com/paper/2303.06274/) (2023)
- [Nuclei instance segmentation and classification in histopathology images with StarDist](https://mlsanity.com/paper/2203.02284/) (2022)
- [NuInsSeg: A Fully Annotated Dataset for Nuclei Instance Segmentation in H&E-Stained Histological Images](https://mlsanity.com/paper/2308.01760/) (2023)
- [Domain Generalization in Computational Pathology: Survey and Guidelines](https://mlsanity.com/paper/2310.19656/) (2023)
- [Deep learning for unsupervised domain adaptation in medical imaging: Recent advancements and future perspectives](https://mlsanity.com/paper/2308.01265/) (2023)
- [STimage-1K4M: A histopathology image-gene expression dataset for spatial transcriptomics](https://mlsanity.com/paper/2406.06393/) (2024)
- [NASDM: Nuclei-Aware Semantic Histopathology Image Generation Using Diffusion Models](https://mlsanity.com/paper/2303.11477/) (2023)
- [Domain Adaptive Nuclei Instance Segmentation and Classification via Category-aware Feature Alignment and Pseudo-labelling](https://mlsanity.com/paper/2207.01233/) (2022)
- [TopoCellGen: Generating Histopathology Cell Topology with a Diffusion Model](https://mlsanity.com/paper/2412.06011/) (2024)
- [mathrmSAMMed: A medical image annotation framework based on large vision model](https://mlsanity.com/paper/2307.05617/) (2023)
- [Affine-Consistent Transformer for Multi-Class Cell Nuclei Detection](https://mlsanity.com/paper/2310.14154/) (2023)
- [PixCell: A generative foundation model for digital histopathology images](https://mlsanity.com/paper/2506.05127/) (2025)
- [Seeing Unseen: Discover Novel Biomedical Concepts via Geometry-Constrained Probabilistic Modeling](https://mlsanity.com/paper/2403.01053/) (2024)
- [Cell Graph Transformer for Nuclei Classification](https://mlsanity.com/paper/2402.12946/) (2024)
- [Segment Anything for Histopathology](https://mlsanity.com/paper/2502.00408/) (2025)
- [Recommendations on test datasets for evaluating AI solutions in pathology](https://mlsanity.com/paper/2204.14226/) (2022)
- [DAWN: Domain-Adaptive Weakly Supervised Nuclei Segmentation via Cross-Task Interactions](https://mlsanity.com/paper/2404.14956/) (2024)
- [Controllable and Efficient Multi-Class Pathology Nuclei Data Augmentation using Text-Conditioned Diffusion Models](https://mlsanity.com/paper/2407.14426/) (2024)
- [Co-synthesis of Histopathology Nuclei Image-Label Pairs using a Context-Conditioned Joint Diffusion Model](https://mlsanity.com/paper/2407.14434/) (2024)
- [Tissue Concepts: supervised foundation models in computational pathology](https://mlsanity.com/paper/2409.03519/) (2024)
- [Taxonomy Adaptive Cross-Domain Adaptation in Medical Imaging via Optimization Trajectory Distillation](https://mlsanity.com/paper/2307.14709/) (2023)
- [Mitosis Detection, Fast and Slow: Robust and Efficient Detection of Mitotic Figures](https://mlsanity.com/paper/2208.12587/) (2022)
- [SynCLay: Interactive Synthesis of Histology Images from Bespoke Cellular Layouts](https://mlsanity.com/paper/2212.13780/) (2022)
- [VOLTA: an Environment-Aware Contrastive Cell Representation Learning for Histopathology](https://mlsanity.com/paper/2303.04696/) (2023)
- [Nucleus-aware Self-supervised Pretraining Using Unpaired Image-to-image Translation for Histopathology Images](https://mlsanity.com/paper/2309.07394/) (2023)
- [Learning to Generalize over Subpartitions for Heterogeneity-aware Domain Adaptive Nuclei Segmentation](https://mlsanity.com/paper/2401.09496/) (2024)
- [Panoptic segmentation with highly imbalanced semantic labels](https://mlsanity.com/paper/2203.11692/) (2022)

## Abstract (arXiv)

The development of deep segmentation models for computational pathology (CPath) can help foster the investigation of interpretable morphological biomarkers. Yet, there is a major bottleneck in the success of such approaches because supervised deep learning models require an abundance of accurately labelled data. This issue is exacerbated in the field of CPath because the generation of detailed annotations usually demands the input of a pathologist to be able to distinguish between different tissue constructs and nuclei. Manually labelling nuclei may not be a feasible approach for collecting large-scale annotated datasets, especially when a single image region can contain thousands of different cells. However, solely relying on automatic generation of annotations will limit the accuracy and reliability of ground truth. Therefore, to help overcome the above challenges, we propose a multi-stage annotation pipeline to enable the collection of large-scale datasets for histology image analysis, with pathologist-in-the-loop refinement steps. Using this pipeline, we generate the largest known nuclear instance segmentation and classification dataset, containing nearly half a million labelled nuclei in H&E stained colon tissue. We have released the dataset and encourage the research community to utilise it to drive forward the development of downstream cell-based models in CPath.