# A Semi-automatic Cell Tracking Process Towards Completing the 4D Atlas of C. elegans Development

arXiv: https://arxiv.org/abs/2207.13611 · HTML: https://mlsanity.com/paper/2207.13611/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 6 of its 21 references that are in the map.
- First posted on arXiv 27 Jul 2022.

## Builds on (most cited first, 6 of 6)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Star-convex Polyhedra for 3D Object Detection and Segmentation in Microscopy](https://mlsanity.com/paper/1908.03636/) (2019)
- [KerGM: Kernelized Graph Matching](https://mlsanity.com/paper/1911.11120/) (2019)
- [An Exact Hypergraph Matching Algorithm for Nuclear Identification in Embryonic Caenorhabditis elegans](https://mlsanity.com/paper/2104.10003/) (2021)

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

- [Cell Tracking in C. elegans with Cell Position Heatmap-Based Alignment and Pairwise Detection](https://mlsanity.com/paper/2403.13412/) (2024)

## Abstract (arXiv)

The nematode Caenorhabditis elegans (C. elegans) is used as a model organism to better understand developmental biology and neurobiology. C. elegans features an invariant cell lineage, which has been catalogued and observed using fluorescence microscopy images. However, established methods to track cells in late-stage development fail to generalize once sporadic muscular twitching has begun. We build upon methodology which uses skin cells as fiducial markers to carry out cell tracking despite random twitching. In particular, we present a cell nucleus segmentation and tracking procedure which was integrated into a 3D rendering GUI to improve efficiency in tracking cells across late-stage development. Results on images depicting aforementioned muscle cell nuclei across three test embryos suggest the fiducial markers in conjunction with a classic tracking paradigm overcome sporadic twitching.