Fig. 2

SpotNGlia semi-automatically counts microglia numbers. (A) Examples of z-stack images of NR-stained larvae and a schematic representation of the SpotNGlia analysis pipeline. (B) SpotNGlia output of test dataset with both manual (blue) and automated (red) brain segmentation and NR⁺ microglia annotation. (C) Box plots showing Jaccard and Dice indices for accuracy of brain segmentation and F1, precision and recall scores for the accuracy of NR⁺microglia annotation. This is a Tukey boxplot: it uses the median and interquartile range (IQR) for the box. The whiskers extend to the most extreme data within 1.5×IQR. Data outside 1.5×IQR are considered outliers. (D) Correlation between manually and automated microglia quantification after manual correction for segmented brain area. Error bars represent s.d.