The software recognizes a very low droplet count, even if I can see that they are more droplets in the chamber

There are several reasons why this could be happening: -the basal fluorescence of the droplets is too low (please check that you have added 100 nM fluorescein), – the droplets are compacted and tend to overlap each other. In that case, place the Sapphire chips back into the Geode, and run the “unstacking.js” script to relax the droplet crystal.