Deep Temporal Sequence Classification and Mathematical Modeling for Cell Tracking in Dense 3D Microscopy Videos of Bacterial Biofilms
This work addresses the challenge of tracking cells in crowded environments like bacterial biofilms, which is crucial for biological research, but it appears incremental as it builds on existing deep learning and optimization techniques.
The paper tackled the problem of automatic cell tracking in dense 3D microscopy videos of bacterial biofilms, which suffers from inaccurate correspondences and misidentification of parent-offspring relationships, and introduced DenseTrack, a novel algorithm that integrates deep learning with mathematical modeling to achieve superior performance compared to recent state-of-the-art methods in both qualitative and quantitative evaluations.
Automatic cell tracking in dense environments is plagued by inaccurate correspondences and misidentification of parent-offspring relationships. In this paper, we introduce a novel cell tracking algorithm named DenseTrack, which integrates deep learning with mathematical model-based strategies to effectively establish correspondences between consecutive frames and detect cell division events in crowded scenarios. We formulate the cell tracking problem as a deep learning-based temporal sequence classification task followed by solving a constrained one-to-one matching optimization problem exploiting the classifier's confidence scores. Additionally, we present an eigendecomposition-based cell division detection strategy that leverages knowledge of cellular geometry. The performance of the proposed approach has been evaluated by tracking densely packed cells in 3D time-lapse image sequences of bacterial biofilm development. The experimental results on simulated as well as experimental fluorescence image sequences suggest that the proposed tracking method achieves superior performance in terms of both qualitative and quantitative evaluation measures compared to recent state-of-the-art cell tracking approaches.