# Practical Guidelines for Cell Segmentation Models Under Optical Aberrations in Microscopy

arXiv: https://arxiv.org/abs/2404.08549 · HTML: https://mlsanity.com/paper/2404.08549/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 15 of its 46 references that are in the map.
- First posted on arXiv 12 Apr 2024.

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

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Swin Transformer: Hierarchical Vision Transformer using Shifted Windows](https://mlsanity.com/paper/2103.14030/) (2021)
- [Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks](https://mlsanity.com/paper/1506.01497/) (2015)
- [Densely Connected Convolutional Networks](https://mlsanity.com/paper/1608.06993/) (2016)
- [EfficientNet: Rethinking Model Scaling for Convolutional Neural Networks](https://mlsanity.com/paper/1905.11946/) (2019)
- [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)
- [MobileNetV2: Inverted Residuals and Linear Bottlenecks](https://mlsanity.com/paper/1801.04381/) (2018)
- [SqueezeNet: AlexNet-level accuracy with 50x fewer parameters and <0.5MB model size](https://mlsanity.com/paper/1602.07360/) (2016)
- [SA-UNet: Spatial Attention U-Net for Retinal Vessel Segmentation](https://mlsanity.com/paper/2004.03696/) (2020)
- [Attention-Based Transformers for Instance Segmentation of Cells in Microstructures](https://mlsanity.com/paper/2011.09763/) (2020)
- [A Multi-Branch Hybrid Transformer Networkfor Corneal Endothelial Cell Segmentation](https://mlsanity.com/paper/2106.07557/) (2021)
- [Mixed-UNet: Refined Class Activation Mapping for Weakly-Supervised Semantic Segmentation with Multi-scale Inference](https://mlsanity.com/paper/2205.04227/) (2022)
- [An Instance Segmentation Dataset of Yeast Cells in Microstructures](https://mlsanity.com/paper/2304.07597/) (2023)

## Built on by (most cited first, 1 of 1)

- [High-Throughput Low-Cost Segmentation of Brightfield Microscopy Live Cell Images](https://mlsanity.com/paper/2508.14106/) (2025)

## Abstract (arXiv)

Cell segmentation is essential in biomedical research for analyzing cellular morphology and behavior. Deep learning methods, particularly convolutional neural networks (CNNs), have revolutionized cell segmentation by extracting intricate features from images. However, the robustness of these methods under microscope optical aberrations remains a critical challenge. This study evaluates cell image segmentation models under optical aberrations from fluorescence and bright field microscopy. By simulating different types of aberrations, including astigmatism, coma, spherical aberration, trefoil, and mixed aberrations, we conduct a thorough evaluation of various cell instance segmentation models using the DynamicNuclearNet (DNN) and LIVECell datasets, representing fluorescence and bright field microscopy cell datasets, respectively. We train and test several segmentation models, including the Otsu threshold method and Mask R-CNN with different network heads (FPN, C3) and backbones (ResNet, VGG, Swin Transformer), under aberrated conditions. Additionally, we provide usage recommendations for the Cellpose 2.0 Toolbox on complex cell degradation images. The results indicate that the combination of FPN and SwinS demonstrates superior robustness in handling simple cell images affected by minor aberrations. In contrast, Cellpose 2.0 proves effective for complex cell images under similar conditions. Furthermore, we innovatively propose the Point Spread Function Image Label Classification Model (PLCM). This model can quickly and accurately identify aberration types and amplitudes from PSF images, assisting researchers without optical training. Through PLCM, researchers can better apply our proposed cell segmentation guidelines.