# Estimation and Analysis of Slice Propagation Uncertainty in 3D Anatomy Segmentation

arXiv: https://arxiv.org/abs/2403.12290 · HTML: https://mlsanity.com/paper/2403.12290/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 19 of its 31 references that are in the map.
- First posted on arXiv 18 Mar 2024.

## Builds on (most cited first, 19 of 19)

- [Dropout as a Bayesian Approximation: Representing Model Uncertainty in Deep Learning](https://mlsanity.com/paper/1506.02142/) (2015)
- [Simple and Scalable Predictive Uncertainty Estimation using Deep Ensembles](https://mlsanity.com/paper/1612.01474/) (2016)
- [What Uncertainties Do We Need in Bayesian Deep Learning for Computer Vision?](https://mlsanity.com/paper/1703.04977/) (2017)
- [Rethinking Atrous Convolution for Semantic Image Segmentation](https://mlsanity.com/paper/1706.05587/) (2017)
- [Averaging Weights Leads to Wider Optima and Better Generalization](https://mlsanity.com/paper/1803.05407/) (2018)
- [A Simple Baseline for Bayesian Uncertainty in Deep Learning](https://mlsanity.com/paper/1902.02476/) (2019)
- [Pseudo-Labeling and Confirmation Bias in Deep Semi-Supervised Learning](https://mlsanity.com/paper/1908.02983/) (2019)
- [Dataset Cartography: Mapping and Diagnosing Datasets with Training Dynamics](https://mlsanity.com/paper/2009.10795/) (2020)
- [A large annotated medical image dataset for the development and evaluation of segmentation algorithms](https://mlsanity.com/paper/1902.09063/) (2019)
- [BatchEnsemble: An Alternative Approach to Efficient Ensemble and Lifelong Learning](https://mlsanity.com/paper/2002.06715/) (2020)
- [Concrete Dropout](https://mlsanity.com/paper/1705.07832/) (2017)
- [The KiTS21 Challenge: Automatic segmentation of kidneys, renal tumors, and renal cysts in corticomedullary-phase CT](https://mlsanity.com/paper/2307.01984/) (2023)
- [Assessing Reliability and Challenges of Uncertainty Estimations for Medical Image Segmentation](https://mlsanity.com/paper/1907.03338/) (2019)
- [Inconsistency-aware Uncertainty Estimation for Semi-supervised Medical Image Segmentation](https://mlsanity.com/paper/2110.08762/) (2021)
- [Uncertain-DeepSSM: From Images to Probabilistic Shape Models](https://mlsanity.com/paper/2007.06516/) (2020)
- [Sli2Vol: Annotate a 3D Volume from a Single Slice with Self-Supervised Learning](https://mlsanity.com/paper/2105.12722/) (2021)
- [Medical Image Segmentation with 3D Convolutional Neural Networks: A Survey](https://mlsanity.com/paper/2108.08467/) (2021)
- [Orthogonal Annotation Benefits Barely-supervised Medical Image Segmentation](https://mlsanity.com/paper/2303.13090/) (2023)
- [Benchmarking Scalable Epistemic Uncertainty Quantification in Organ Segmentation](https://mlsanity.com/paper/2308.07506/) (2023)

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

- [On the Viability of Semi-Supervised Segmentation Methods for Statistical Shape Modeling](https://mlsanity.com/paper/2407.15260/) (2024)
- [Inference-Time Orthogonal Seeding Enables Geometry-Aligned 3D Organ Segmentation for Slice-Propagation Methods](https://mlsanity.com/paper/2608.12658/) (2026)

## Abstract (arXiv)

Supervised methods for 3D anatomy segmentation demonstrate superior performance but are often limited by the availability of annotated data. This limitation has led to a growing interest in self-supervised approaches in tandem with the abundance of available un-annotated data. Slice propagation has emerged as an self-supervised approach that leverages slice registration as a self-supervised task to achieve full anatomy segmentation with minimal supervision. This approach significantly reduces the need for domain expertise, time, and the cost associated with building fully annotated datasets required for training segmentation networks. However, this shift toward reduced supervision via deterministic networks raises concerns about the trustworthiness and reliability of predictions, especially when compared with more accurate supervised approaches. To address this concern, we propose the integration of calibrated uncertainty quantification (UQ) into slice propagation methods, providing insights into the model's predictive reliability and confidence levels. Incorporating uncertainty measures enhances user confidence in self-supervised approaches, thereby improving their practical applicability. We conducted experiments on three datasets for 3D abdominal segmentation using five UQ methods. The results illustrate that incorporating UQ improves not only model trustworthiness, but also segmentation accuracy. Furthermore, our analysis reveals various failure modes of slice propagation methods that might not be immediately apparent to end-users. This study opens up new research avenues to improve the accuracy and trustworthiness of slice propagation methods.