It's actually inferred by hardware - the paper handwaves it because they wanted to focus on the software, but basically they're talking about implementing a low-accuracy micro-ADC at every site that automatically wipes the charge when it hits a trigger voltage and counts every time it does so. Number of counts = site signal level.

Not quite sure that's practical or how you'd implement it on a destructive-readout sensor, though. Right now the sensors with enough accuracy and sensitivity are all destructive.