Adaptive tracking algorithm for trajectory analysis of cells and layer-by-layer assessment of motility dynamics


Qureshi M. H., Ozlu N., Bayraktar H.

COMPUTERS IN BIOLOGY AND MEDICINE, vol.150, 2022 (SCI-Expanded) identifier identifier

  • Publication Type: Article / Article
  • Volume: 150
  • Publication Date: 2022
  • Doi Number: 10.1016/j.compbiomed.2022.106193
  • Journal Name: COMPUTERS IN BIOLOGY AND MEDICINE
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Academic Search Premier, Applied Science & Technology Source, BIOSIS, Biotechnology Research Abstracts, CINAHL, Compendex, Computer & Applied Sciences, EMBASE, INSPEC, Library, Information Science & Technology Abstracts (LISTA), MEDLINE
  • Keywords: Tracking, Segmentation, Algorithms, Image processing, Cell trajectories, Linkage analysis, Networks, Open source software, Motility dynamics, Single cell, CONTRAST VIDEO MICROSCOPY, SINGLE-PARTICLE TRACKING, AUTOMATIC SEGMENTATION, IN-VITRO, QUANTITATIVE-ANALYSIS, MIGRATING CELLS, LEVEL SETS, NUCLEI, CYCLE, TOOLS
  • Istanbul Technical University Affiliated: Yes

Abstract

Tracking biological objects such as cells or subcellular components imaged with time-lapse microscopy enables us to understand the molecular principles about the dynamics of cell behaviors. However, automatic object detection, segmentation and extracting trajectories remain as a rate-limiting step due to intrinsic challenges of video processing. This paper presents an adaptive tracking algorithm (Adtari) that automatically finds the op-timum search radius and cell linkages to determine trajectories in consecutive frames. A critical assumption in most tracking studies is that displacement remains unchanged throughout the movie and cells in a few frames are usually analyzed to determine its magnitude. Tracking errors and inaccurate association of cells may occur if the user does not correctly evaluate the value or prior knowledge is not present on cell movement. The key novelty of our method is that minimum intercellular distance and maximum displacement of cells between frames are dynamically computed and used to determine the threshold distance. Since the space between cells is highly variable in a given frame, our software recursively alters the magnitude to determine all plausible matches in the trajectory analysis. Our method therefore eliminates a major preprocessing step where a constant distance was used to determine the neighbor cells in tracking methods. Cells having multiple overlaps and splitting events were further evaluated by using the shape attributes including perimeter, area, ellipticity and distance. The features were applied to determine the closest matches by minimizing the difference in their magnitudes. Finally, reporting section of our software were used to generate instant maps by overlaying cell features and trajectories. Adtari was validated by using videos with variable signal-to-noise, contrast ratio and cell density. We compared the adaptive tracking with constant distance and other methods to evaluate performance and its efficiency. Our algorithm yields reduced mismatch ratio, increased ratio of whole cell track, higher frame tracking efficiency and allows layer-by-layer assessment of motility to characterize single-cells. Adaptive tracking provides a reliable, accurate, time efficient and user-friendly open source software that is well suited for analysis of 2D fluorescence microscopy video datasets.