# Understanding the Tricks of Deep Learning in Medical Image Segmentation: Challenges and Future Directions

arXiv: https://arxiv.org/abs/2209.10307 · HTML: https://mlsanity.com/paper/2209.10307/

## Key facts

- Cited by 5 papers in the map (data through 14 Oct 2026).
- Builds on 132 of its 228 references that are in the map.
- First posted on arXiv 21 Sep 2022.

## Builds on (most cited first, 30 of 132)

- [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)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [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)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift](https://mlsanity.com/paper/1502.03167/) (2015)
- [Densely Connected Convolutional Networks](https://mlsanity.com/paper/1608.06993/) (2016)
- [Layer Normalization](https://mlsanity.com/paper/1607.06450/) (2016)
- [Feature Pyramid Networks for Object Detection](https://mlsanity.com/paper/1612.03144/) (2016)
- [Fully Convolutional Networks for Semantic Segmentation](https://mlsanity.com/paper/1411.4038/) (2014)
- [Squeeze-and-Excitation Networks](https://mlsanity.com/paper/1709.01507/) (2017)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Training data-efficient image transformers & distillation through attention](https://mlsanity.com/paper/2012.12877/) (2020)
- [Image-to-Image Translation with Conditional Adversarial Networks](https://mlsanity.com/paper/1611.07004/) (2016)
- [Going Deeper with Convolutions](https://mlsanity.com/paper/1409.4842/) (2014)
- [MobileNets: Efficient Convolutional Neural Networks for Mobile Vision Applications](https://mlsanity.com/paper/1704.04861/) (2017)
- [DeepLab: Semantic Image Segmentation with Deep Convolutional Nets, Atrous Convolution, and Fully Connected CRFs](https://mlsanity.com/paper/1606.00915/) (2016)
- [Encoder-Decoder with Atrous Separable Convolution for Semantic Image Segmentation](https://mlsanity.com/paper/1802.02611/) (2018)
- [Exploring Simple Siamese Representation Learning](https://mlsanity.com/paper/2011.10566/) (2020)
- [Aggregated Residual Transformations for Deep Neural Networks](https://mlsanity.com/paper/1611.05431/) (2016)
- [Pyramid Scene Parsing Network](https://mlsanity.com/paper/1612.01105/) (2016)
- [Non-local Neural Networks](https://mlsanity.com/paper/1711.07971/) (2017)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [Learning to Prompt for Vision-Language Models](https://mlsanity.com/paper/2109.01134/) (2021)

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

- [LISA++: An Improved Baseline for Reasoning Segmentation with Large Language Model](https://mlsanity.com/paper/2312.17240/) (2023)
- [Dynamic Pseudo Label Optimization in Point-Supervised Nuclei Segmentation](https://mlsanity.com/paper/2406.16427/) (2024)
- [Merging Context Clustering with Visual State Space Models for Medical Image Segmentation](https://mlsanity.com/paper/2501.01618/) (2025)
- [Topology-Aware Wavelet Mamba for Airway Structure Segmentation in Postoperative Recurrent Nasopharyngeal Carcinoma CT Scans](https://mlsanity.com/paper/2502.14363/) (2025)
- [Wave-GMS: Lightweight Multi-Scale Generative Model for Medical Image Segmentation](https://mlsanity.com/paper/2510.03216/) (2025)

## Abstract (arXiv)

Over the past few years, the rapid development of deep learning technologies for computer vision has significantly improved the performance of medical image segmentation (MedISeg). However, the diverse implementation strategies of various models have led to an extremely complex MedISeg system, resulting in a potential problem of unfair result comparisons. In this paper, we collect a series of MedISeg tricks for different model implementation phases (i.e., pre-training model, data pre-processing, data augmentation, model implementation, model inference, and result post-processing), and experimentally explore the effectiveness of these tricks on consistent baselines. With the extensive experimental results on both the representative 2D and 3D medical image datasets, we explicitly clarify the effect of these tricks. Moreover, based on the surveyed tricks, we also open-sourced a strong MedISeg repository, where each component has the advantage of plug-and-play. We believe that this milestone work not only completes a comprehensive and complementary survey of the state-of-the-art MedISeg approaches, but also offers a practical guide for addressing the future medical image processing challenges including but not limited to small dataset, class imbalance learning, multi-modality learning, and domain adaptation. The code and training weights have been released at: https://github.com/hust-linyi/seg_trick.