Fig. 5: Rapid high-resolution reconstruction of 2-day-long monitoring of inflammatory dynamics in zebrafish with more than 345,600 volumes.
a, Bright-field image depicting the zebrafish tailfin injury. b, Dual-directional MIPs of neutrophils (yellow) and macrophages (green) migrating in the vasculature, obtained by SeReNet. c,d, Comparison of volume numbers reconstructed within 48 h (c) and total processing time for the whole sequence (d). e, Shown are 70° MIPs comparing different reconstruction methods. Illustrative cell segmentations using CellPose are plotted below. f, Boxplot showing counts of cell segmentations. n = 201 images at different times. P = 1.07 × 10−151. g, Tracked traces of cells by SeReNet during inflammatory process. All cells (n = 1,531) were counted. h, Maps of average local cell densities (left) and velocities (right) along the x and y directions over time in injured zebrafish. i, Tracked traces of cells by SeReNet in non-injured zebrafish. All cells (n = 806) were counted. j, Maps of average local cell densities (left) and velocities (right) along the x and y directions over time in non-injured zebrafish. k,l, Curves of neutrophil (k) and macrophage (l) flow quantities over time. m, Increased rate in cell quantities for neutrophils and macrophages, calculated as the ratio of the cell number in the injured state to the non-injured state; data were normalized to t = 0 h. n,o, Curves of adjacent distances between neutrophils (n) and macrophages (o) over time. The adjacent distance of each cell is defined as the average distance between the ten cells closest to it. Data are represented as mean ± s.d. p,q, Violin plot of mean velocities of neutrophils (p) and macrophages (q). Mean velocity (μm s–1) was calculated for individual tracks by linear regression of trajectory lengths versus time. n represents the cell number. n = 828 (neutrophil, injured), n = 284 (neutrophil, non-injured), n = 703 (macrophage, injured), n = 522 (macrophage, non-injured). P = 2.30 × 10−154, 2.13 × 10−19. The boxplot formats: center line, median; box limits, lower and upper quartiles; whiskers, 1.5 × interquartile range. Asterisks represent significance levels tested with two-sided paired t-test; significance was set at P < 0.05. ****P < 1 × 10−4. SeReNet was the axially improved version and was trained on synthetic bubtub dataset. Scale bars, 100 μm (a,b,e,g,i).
