We have been working with zebrafish larvae as a model system for human diseases for a while, and have recently showed that they are excellent systems to study development of leukaemia. Fluorescently labelled leukaemia cells can be transplanted into the larvae by intravenous injection. In a recently published paper, we have written a software plug-in which automatically counts the number of individual leukaemia cells based on confocal microscopy images. In this way, we can follow how the leukaemia develops, both over time, and how they distribute in the larvae. Although tailor-made for larvae transplanted with leukaemia cells, the software can be used to analyze any fluorescent particle. This work was recently published in Biology open.