# From Histopathology Images to Cell Clouds: Learning Slide Representations with Hierarchical Cell Transformer

arXiv: https://arxiv.org/abs/2412.16715 · HTML: https://mlsanity.com/paper/2412.16715/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 36 of its 60 references that are in the map.
- First posted on arXiv 21 Dec 2024.

## Builds on (most cited first, 30 of 36)

- [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)
- [PointNet: Deep Learning on Point Sets for 3D Classification and Segmentation](https://mlsanity.com/paper/1612.00593/) (2016)
- [PointNet++: Deep Hierarchical Feature Learning on Point Sets in a Metric Space](https://mlsanity.com/paper/1706.02413/) (2017)
- [ScanNet: Richly-annotated 3D Reconstructions of Indoor Scenes](https://mlsanity.com/paper/1702.04405/) (2017)
- [PointPillars: Fast Encoders for Object Detection from Point Clouds](https://mlsanity.com/paper/1812.05784/) (2018)
- [Point Transformer](https://mlsanity.com/paper/2011.00931/) (2020)
- [4D Spatio-Temporal ConvNets: Minkowski Convolutional Neural Networks](https://mlsanity.com/paper/1904.08755/) (2019)
- [Attention-based Deep Multiple Instance Learning](https://mlsanity.com/paper/1802.04712/) (2018)
- [On the Variance of the Adaptive Learning Rate and Beyond](https://mlsanity.com/paper/1908.03265/) (2019)
- [3D Semantic Segmentation with Submanifold Sparse Convolutional Networks](https://mlsanity.com/paper/1711.10275/) (2017)
- [Data Efficient and Weakly Supervised Computational Pathology on Whole Slide Images](https://mlsanity.com/paper/2004.09666/) (2020)
- [Point Transformer V3: Simpler, Faster, Stronger](https://mlsanity.com/paper/2312.10035/) (2023)
- [TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classification](https://mlsanity.com/paper/2106.00908/) (2021)
- [HoVer-Net: Simultaneous Segmentation and Classification of Nuclei in Multi-Tissue Histology Images](https://mlsanity.com/paper/1812.06499/) (2018)
- [Point Transformer V2: Grouped Vector Attention and Partition-based Pooling](https://mlsanity.com/paper/2210.05666/) (2022)
- [Rethinking Network Design and Local Geometry in Point Cloud: A Simple Residual MLP Framework](https://mlsanity.com/paper/2202.07123/) (2022)
- [Scaling Vision Transformers to Gigapixel Images via Hierarchical Self-Supervised Learning](https://mlsanity.com/paper/2206.02647/) (2022)
- [Quilt-1M: One Million Image-Text Pairs for Histopathology](https://mlsanity.com/paper/2306.11207/) (2023)
- [PointMamba: A Simple State Space Model for Point Cloud Analysis](https://mlsanity.com/paper/2402.10739/) (2024)
- [Whole Slide Images are 2D Point Clouds: Context-Aware Survival Prediction using Patch-based Graph Convolutional Networks](https://mlsanity.com/paper/2107.13048/) (2021)
- [PanNuke Dataset Extension, Insights and Baselines](https://mlsanity.com/paper/2003.10778/) (2020)
- [OctFormer: Octree-based Transformers for 3D Point Clouds](https://mlsanity.com/paper/2305.03045/) (2023)
- [Modeling Dense Multimodal Interactions Between Biological Pathways and Histology for Survival Prediction](https://mlsanity.com/paper/2304.06819/) (2023)
- [Interventional Bag Multi-Instance Learning On Whole-Slide Pathological Images](https://mlsanity.com/paper/2303.06873/) (2023)
- [Lizard: A Large-Scale Dataset for Colonic Nuclear Instance Segmentation and Classification](https://mlsanity.com/paper/2108.11195/) (2021)
- [Methods for Segmentation and Classification of Digital Microscopy Tissue Images](https://mlsanity.com/paper/1810.13230/) (2018)
- [LargeKernel3D: Scaling up Kernels in 3D Sparse CNNs](https://mlsanity.com/paper/2206.10555/) (2022)
- [Morphological Prototyping for Unsupervised Slide Representation Learning in Computational Pathology](https://mlsanity.com/paper/2405.11643/) (2024)
- [Dynamic Graph Representation with Knowledge-aware Attention for Histopathology Whole Slide Image Analysis](https://mlsanity.com/paper/2403.07719/) (2024)

## Built on by (most cited first, 2 of 2)

- [Towards Effective and Efficient Context-aware Nucleus Detection in Histopathology Whole Slide Images](https://mlsanity.com/paper/2503.05678/) (2025)
- [NuNext: Reframing Nucleus Detection as Next-Point Detection](https://mlsanity.com/paper/2603.07098/) (2026)

## Abstract (arXiv)

It is clinically crucial and potentially very beneficial to be able to analyze and model directly the spatial distributions of cells in histopathology whole slide images (WSI). However, most existing WSI datasets lack cell-level annotations, owing to the extremely high cost over giga-pixel images. Thus, it remains an open question whether deep learning models can directly and effectively analyze WSIs from the semantic aspect of cell distributions. In this work, we construct a large-scale WSI dataset with more than 5 billion cell-level annotations, termed WSI-Cell5B, and a novel hierarchical Cell Cloud Transformer (CCFormer) to tackle these challenges. WSI-Cell5B is based on 6,998 WSIs of 11 cancers from The Cancer Genome Atlas Program, and all WSIs are annotated per cell by coordinates and types. To the best of our knowledge, WSI-Cell5B is the first WSI-level large-scale dataset integrating cell-level annotations. On the other hand, CCFormer formulates the collection of cells in each WSI as a cell cloud and models cell spatial distribution. Specifically, Neighboring Information Embedding (NIE) is proposed to characterize the distribution of cells within the neighborhood of each cell, and a novel Hierarchical Spatial Perception (HSP) module is proposed to learn the spatial relationship among cells in a bottom-up manner. The clinical analysis indicates that WSI-Cell5B can be used to design clinical evaluation metrics based on counting cells that effectively assess the survival risk of patients. Extensive experiments on survival prediction and cancer staging show that learning from cell spatial distribution alone can already achieve state-of-the-art (SOTA) performance, i.e., CCFormer strongly outperforms other competing methods.