An Image Processing Tool for Automated Quantification of Bacterial Burdens in Zebrafish Larvae

Zebrafish larvae are used to model the pathogenesis of multiple bacteria. This transparent model offers the unique advantage of allowing quantification of fluorescent bacterial burdens (fluorescent pixel counts [FPC]) <i>in vivo</i> by facile microscopical methods, replacing enumeration of bacteria using time-intensive plating of lysates on bacteriological media. Accurate FPC measurements require laborious manual image processing to mark the outside borders of the animals so as to delineate the bacteria inside the animals from those in the culture medium that they are in. Here, we have developed an automated ImageJ/Fiji-based macro that accurately detects the outside borders of <i>Mycobacterium marinum</i>-infected larvae.