# Neural Annotation Refinement: Development of a New 3D Dataset for Adrenal Gland Analysis

arXiv: https://arxiv.org/abs/2206.15328 · HTML: https://mlsanity.com/paper/2206.15328/

## Key facts

- Cited by 5 papers in the map (data through 14 Oct 2026).
- Builds on 23 of its 32 references that are in the map.
- First posted on arXiv 30 Jun 2022.

## Builds on (most cited first, 23 of 23)

- [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)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Fully Convolutional Networks for Semantic Segmentation](https://mlsanity.com/paper/1411.4038/) (2014)
- [DeepSDF: Learning Continuous Signed Distance Functions for Shape Representation](https://mlsanity.com/paper/1901.05103/) (2019)
- [Occupancy Networks: Learning 3D Reconstruction in Function Space](https://mlsanity.com/paper/1812.03828/) (2018)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Deep Image Prior](https://mlsanity.com/paper/1711.10925/) (2017)
- [Learning Implicit Fields for Generative Shape Modeling](https://mlsanity.com/paper/1812.02822/) (2018)
- [GIRAFFE: Representing Scenes as Compositional Generative Neural Feature Fields](https://mlsanity.com/paper/2011.12100/) (2020)
- [Convolutional Occupancy Networks](https://mlsanity.com/paper/2003.04618/) (2020)
- [MedMNIST v2 -- A large-scale lightweight benchmark for 2D and 3D biomedical image classification](https://mlsanity.com/paper/2110.14795/) (2021)
- [Implicit Functions in Feature Space for 3D Shape Reconstruction and Completion](https://mlsanity.com/paper/2003.01456/) (2020)
- [DISN: Deep Implicit Surface Network for High-quality Single-view 3D Reconstruction](https://mlsanity.com/paper/1905.10711/) (2019)
- [Embracing Imperfect Datasets: A Review of Deep Learning Solutions for Medical Image Segmentation](https://mlsanity.com/paper/1908.10454/) (2019)
- [AbdomenCT-1K: Is Abdominal Organ Segmentation A Solved Problem?](https://mlsanity.com/paper/2010.14808/) (2020)
- [Deep learning with noisy labels: exploring techniques and remedies in medical image analysis](https://mlsanity.com/paper/1912.02911/) (2019)
- [DeepCut: Object Segmentation from Bounding Box Annotations using Convolutional Neural Networks](https://mlsanity.com/paper/1605.07866/) (2016)
- [Deep learning to achieve clinically applicable segmentation of head and neck anatomy for radiotherapy](https://mlsanity.com/paper/1809.04430/) (2018)
- [IntrA: 3D Intracranial Aneurysm Dataset for Deep Learning](https://mlsanity.com/paper/2003.02920/) (2020)
- [Point2Mesh: A Self-Prior for Deformable Meshes](https://mlsanity.com/paper/2005.11084/) (2020)
- [RibSeg Dataset and Strong Point Cloud Baselines for Rib Segmentation from CT Scans](https://mlsanity.com/paper/2109.09521/) (2021)
- [Representation-Agnostic Shape Fields](https://mlsanity.com/paper/2203.10259/) (2022)

## Built on by (most cited first, 5 of 5)

- [Approaching Peak Ground Truth](https://mlsanity.com/paper/2301.00243/) (2022)
- [Topology Repairing of Disconnected Pulmonary Airways and Vessels: Baselines and a Dataset](https://mlsanity.com/paper/2306.07089/) (2023)
- [Template-Guided Reconstruction of Pulmonary Segments with Neural Implicit Functions](https://mlsanity.com/paper/2505.08919/) (2025)
- [End-to-End Learning of Multi-Organ Implicit Surfaces from 3D Medical Imaging Data](https://mlsanity.com/paper/2509.12068/) (2025)
- [Refining 3D Medical Segmentation with Verbal Instruction](https://mlsanity.com/paper/2603.14496/) (2026)

## Abstract (arXiv)

The human annotations are imperfect, especially when produced by junior practitioners. Multi-expert consensus is usually regarded as golden standard, while this annotation protocol is too expensive to implement in many real-world projects. In this study, we propose a method to refine human annotation, named Neural Annotation Refinement (NeAR). It is based on a learnable implicit function, which decodes a latent vector into represented shape. By integrating the appearance as an input of implicit functions, the appearance-aware NeAR fixes the annotation artefacts. Our method is demonstrated on the application of adrenal gland analysis. We first show that the NeAR can repair distorted golden standards on a public adrenal gland segmentation dataset. Besides, we develop a new Adrenal gLand ANalysis (ALAN) dataset with the proposed NeAR, where each case consists of a 3D shape of adrenal gland and its diagnosis label (normal vs. abnormal) assigned by experts. We show that models trained on the shapes repaired by the NeAR can diagnose adrenal glands better than the original ones. The ALAN dataset will be open-source, with 1,584 shapes for adrenal gland diagnosis, which serves as a new benchmark for medical shape analysis. Code and dataset are available at https://github.com/M3DV/NeAR.