Supporting data for: Characterizing trajectories of innate immune cells in larval zebrafish (PRX Life)

This dataset contains trajectory and subtrack data for neutrophils and macrophages from experiments tracking innate immune cell dynamics in larval zebrafish. The data supports the manuscript "Characterizing trajectories of innate immune cells in larval zebrafish" by Amitabh and Parthasarathy, published in PRX Life (2026). Citation: Amitabh, P. & Parthasarathy, R. (2026). Characterizing trajectories of innate immune cells in larval zebrafish. PRX Life. https://doi.org/10.1103/wx8f-b1p9 The dataset includes eight CSV files total: EXPERIMENTAL DATASETS (4 files):1. gut neutrophil track data simplified.csv - Trajectory and subtrack data for neutrophils from gut bacterial association experiments2. gut macrophage track data simplified.csv - Trajectory and subtrack data for macrophages from gut bacterial association experiments3. fin cut assay neutrophil track data simplified.csv - Trajectory and subtrack data for neutrophils from fin cut assay experiments4. fin cut assay macrophage track data simplified.csv - Trajectory and subtrack data for macrophages from fin cut assay experiments SIMULATED DATASETS (4 files):1. simulated gut neutrophil track data.csv - Simulated trajectory data for neutrophils (gut experiments)2. simulated gut macrophage track data.csv - Simulated trajectory data for macrophages (gut experiments)3. simulated fin cut assay neutrophil track data.csv - Simulated trajectory data for neutrophils (fin cut assay)4. simulated fin cut assay macrophage track data.csv - Simulated trajectory data for macrophages (fin cut assay) Each CSV file contains the following columns:- track_id: Unique identifier for each complete cell trajectory- subtrack_id: Unique identifier for trajectory subdivisions based on motility state transitions- time_point: Frame number in the time series- slice: Z, Y, X-slice position in the image stack (numpy array slicing convention)- fish_id: Unique identifier for each zebrafish with experimental group information- dpf: Days post fertilization at time of imaging Imaging was performed using light sheet fluorescence microscopy at few-minute temporal resolution over multi-hour timescales. Simulated datasets replicate experimental imaging conditions with Gaussian localization noise (σxy = 0.21 µm, σz = 0.43 µm) and quantization to imaging pixel resolution (0.5 µm in xy, 1.0 µm in z). The data enables analysis of immune cell speeds, directional persistence, motility states, and morphological changes in response to various microbiome conditions and tissue damage.