Fig. 5

a Schematic showing the brain regions captured by calcium imaging. Two z-planes in the 6 dpf larval brain were imaged using the genetically encoded calcium indicator neurod:GCaMP6f. b–e Scatter bar charts show the number of spontaneous calcium transients in the corresponding brain regions as illustrated for baseline and after macrophage-rescue. Cerebellum and tectum were each divided into six regions for analysis as depicted in each cartoon. As indicated, calcium transients were calculated on an individual neuron or region basis, or per animal basis using the average calcium transient number of the neurons or region of analysis. The only significant difference found in nlrc3l mutants compared with control siblings was an increase in tectal neuronal calcium transients, which was reversed after macrophage rescue. f Traces from representative individuals of each genotype showing calcium activity (GCaMP6f+) from each of the six tectal regions (1–6) analyzed. Plots show an apparent increase in spiking events in the nlrc3l mutant at baseline. g Relative intracellular calcium levels in the telencephalon and diencephalon (dotted region) at baseline were determined. nlrc3l mutants had consistently lower intracellular calcium in diencephalic neurons corresponding to the dorsal thalamus compared with control siblings, but this was reversible by the macrophage rescue. Arrows point to neurons with robust somatic calcium levels (high GCaMP6f+). h Bar charts show relative intracellular calcium levels in the telencephalon and the diencephalon as an average over the neurons analyzed for each respective region. Each data point represents an individual animal. No difference was determined in intracellular calcium level in the telencephalic neurons based on genotype, but diencephalic neurons were found to have significantly lower intracellular calcium in nlrc3l mutants compared with control siblings. ns, not significant. Two-tailed t-test was used to determine statistical significance. See also associated Supplementary Fig. 8 and Supplementary Movies 6 and 7.