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  • Open Access

Characterizing Trajectories of Innate Immune Cells in Larval Zebrafish

Piyush Amitabh* and Raghuveer Parthasarathy†

  • *Contact author: pamitabh@uoregon.edu
  • †Contact author: raghu@uoregon.edu
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PRX Life 4, 013035 – Published 20 March, 2026

DOI: https://doi.org/10.1103/wx8f-b1p9

Abstract

It is well established from in vitro studies of immune cells that stimulation by a wide range of potential signals leads to motility and morphology changes. How these physical behaviors manifest inside a living animal remains unclear due to limitations of conventional imaging and analysis approaches. Here, we establish a quantitative framework for imaging and tracking neutrophil and macrophage dynamics in larval zebrafish, spanning a large fraction of the animal for multihour timescales with few-minute temporal resolution. We focus especially on the gut, examining innate immune responses to different preparations of the intestinal microbiome. Using light sheet fluorescence microscopy and trajectory analysis of hundreds of individual cells, we characterize speeds, directional persistence measures, and cellular morphology to reveal distinct population behaviors. Individual immune cells exhibit stable motility phenotypes, favoring predominantly motile or nonmotile states rather than frequent transitions between them. Gut architecture constrains migration patterns as demonstrated by preferential anterior-posterior movement and a high probability of cells remaining in the vicinity of the gut throughout the imaging duration. Macrophages display significantly reduced sphericity during motile periods compared to nonmotile periods, providing a morphological signature that may enable inference of dynamic behavior from static snapshots. Surprisingly, migration patterns remain consistent across diverse microbial conditions—germ-free, conventionally reared, and colonized by two strains of a zebrafish-native Vibrio species—indicating that tissue structure exerts a stronger influence than bacterial stimuli on immune surveillance dynamics. Previously observed tissue damage by the wild-type Vibrio strain, and the resulting recruitment of immune cells toward the damage site, provide the only microbe-specific cellular behavior. These findings reveal innate immune surveillance as a stereotyped process whose characteristics reflect both cellular decision-making and larger-scale anatomical structure.

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PRX Life 4, 013035– Published 20 March, 2026
  • Received 13 August 2025
  • Accepted 9 February 2026
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