# Accurate Tracking of Arabidopsis Root Cortex Cell Nuclei in 3D Time-Lapse Microscopy Images Based on Genetic Algorithm

arXiv: https://arxiv.org/abs/2504.12676 · HTML: https://mlsanity.com/paper/2504.12676/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 18 of its 53 references that are in the map.
- First posted on arXiv 17 Apr 2025.

## Builds on (most cited first, 18 of 18)

- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Faster R-CNN: Towards Real-Time Object Detection with Region Proposal Networks](https://mlsanity.com/paper/1506.01497/) (2015)
- [End-to-End Object Detection with Transformers](https://mlsanity.com/paper/2005.12872/) (2020)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [YOLOv3: An Incremental Improvement](https://mlsanity.com/paper/1804.02767/) (2018)
- [Objects as Points](https://mlsanity.com/paper/1904.07850/) (2019)
- [Simple Online and Realtime Tracking](https://mlsanity.com/paper/1602.00763/) (2016)
- [TrackFormer: Multi-Object Tracking with Transformers](https://mlsanity.com/paper/2101.02702/) (2021)
- [FairMOT: On the Fairness of Detection and Re-Identification in Multiple Object Tracking](https://mlsanity.com/paper/2004.01888/) (2020)
- [Tracking without bells and whistles](https://mlsanity.com/paper/1903.05625/) (2019)
- [TransTrack: Multiple Object Tracking with Transformer](https://mlsanity.com/paper/2012.15460/) (2020)
- [Detect to Track and Track to Detect](https://mlsanity.com/paper/1710.03958/) (2017)
- [FAMNet: Joint Learning of Feature, Affinity and Multi-dimensional Assignment for Online Multiple Object Tracking](https://mlsanity.com/paper/1904.04989/) (2019)
- [RANet: Ranking Attention Network for Fast Video Object Segmentation](https://mlsanity.com/paper/1908.06647/) (2019)
- [Online Multi-Target Tracking Using Recurrent Neural Networks](https://mlsanity.com/paper/1604.03635/) (2016)
- [MPM: Joint Representation of Motion and Position Map for Cell Tracking](https://mlsanity.com/paper/2002.10749/) (2020)
- [Large-Scale Multi-Hypotheses Cell Tracking Using Ultrametric Contours Maps](https://mlsanity.com/paper/2308.04526/) (2023)
- [Moral Lineage Tracing](https://mlsanity.com/paper/1511.05512/) (2015)

## Abstract (arXiv)

Arabidopsis is a widely used model plant to gain basic knowledge on plant physiology and development. Live imaging is an important technique to visualize and quantify elemental processes in plant development. To uncover novel theories underlying plant growth and cell division, accurate cell tracking on live imaging is of utmost importance. The commonly used cell tracking software, TrackMate, adopts tracking-by-detection fashion, which applies Laplacian of Gaussian (LoG) for blob detection, and Linear Assignment Problem (LAP) tracker for tracking. However, they do not perform sufficiently when cells are densely arranged. To alleviate the problems mentioned above, we propose an accurate tracking method based on Genetic algorithm (GA) using knowledge of Arabidopsis root cellular patterns and spatial relationship among volumes. Our method can be described as a coarse-to-fine method, in which we first conducted relatively easy line-level tracking of cell nuclei, then performed complicated nuclear tracking based on known linear arrangement of cell files and their spatial relationship between nuclei. Our method has been evaluated on a long-time live imaging dataset of Arabidopsis root tips, and with minor manual rectification, it accurately tracks nuclei. To the best of our knowledge, this research represents the first successful attempt to address a long-standing problem in the field of time-lapse microscopy in the root meristem by proposing an accurate tracking method for Arabidopsis root nuclei.