# A Bilayer Segmentation-Recombination Network for Accurate Segmentation of Overlapping C. elegans

arXiv: https://arxiv.org/abs/2411.17557 · HTML: https://mlsanity.com/paper/2411.17557/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 14 of its 25 references that are in the map.
- First posted on arXiv 26 Nov 2024.

## Builds on (most cited first, 14 of 14)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [CBAM: Convolutional Block Attention Module](https://mlsanity.com/paper/1807.06521/) (2018)
- [YOLACT: Real-time Instance Segmentation](https://mlsanity.com/paper/1904.02689/) (2019)
- [Mask Scoring R-CNN](https://mlsanity.com/paper/1903.00241/) (2019)
- [SegNeXt: Rethinking Convolutional Attention Design for Semantic Segmentation](https://mlsanity.com/paper/2209.08575/) (2022)
- [Deep Occlusion-Aware Instance Segmentation with Overlapping BiLayers](https://mlsanity.com/paper/2103.12340/) (2021)
- [Amodal Instance Segmentation](https://mlsanity.com/paper/1604.08202/) (2016)
- [Learning to See the Invisible: End-to-End Trainable Amodal Instance Segmentation](https://mlsanity.com/paper/1804.08864/) (2018)
- [Amodal Segmentation Based on Visible Region Segmentation and Shape Prior](https://mlsanity.com/paper/2012.05598/) (2020)
- [Segment Any Mesh](https://mlsanity.com/paper/2408.13679/) (2024)
- [Amodal Segmentation through Out-of-Task and Out-of-Distribution Generalization with a Bayesian Model](https://mlsanity.com/paper/2010.13175/) (2020)
- [Efficient 3D Instance Mapping and Localization with Neural Fields](https://mlsanity.com/paper/2403.19797/) (2024)
- [Celeganser: Automated Analysis of Nematode Morphology and Age](https://mlsanity.com/paper/2005.04884/) (2020)
- [Semantic Segmentation Using Deep Learning to Extract Total Extraocular Muscles and Optic Nerve from Orbital Computed Tomography Images](https://mlsanity.com/paper/2007.02091/) (2020)

## Abstract (arXiv)

Caenorhabditis elegans (C. elegans) is an excellent model organism because of its short lifespan and high degree of homology with human genes, and it has been widely used in a variety of human health and disease models. However, the segmentation of C. elegans remains challenging due to the following reasons: 1) the activity trajectory of C. elegans is uncontrollable, and multiple nematodes often overlap, resulting in blurred boundaries of C. elegans. This makes it impossible to clearly study the life trajectory of a certain nematode; and 2) in the microscope images of overlapping C. elegans, the translucent tissues at the edges obscure each other, leading to inaccurate boundary segmentation. To solve these problems, a Bilayer Segmentation-Recombination Network (BR-Net) for the segmentation of C. elegans instances is proposed. The network consists of three parts: A Coarse Mask Segmentation Module (CMSM), a Bilayer Segmentation Module (BSM), and a Semantic Consistency Recombination Module (SCRM). The CMSM is used to extract the coarse mask, and we introduce a Unified Attention Module (UAM) in CMSM to make CMSM better aware of nematode instances. The Bilayer Segmentation Module (BSM) segments the aggregated C. elegans into overlapping and non-overlapping regions. This is followed by integration by the SCRM, where semantic consistency regularization is introduced to segment nematode instances more accurately. Finally, the effectiveness of the method is verified on the C. elegans dataset. The experimental results show that BR-Net exhibits good competitiveness and outperforms other recently proposed instance segmentation methods in processing C. elegans occlusion images.