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It is important to use a PMT transimpedance amplifier with ~ 30-60 MHz bandwidth. Your single photon response should be on the order of 25-40 ns FWHM (for ScanImage2016).
Femo sells appropriate amplifiers.
The TIA60 from Thorlabs works well (https://www.thorlabs.com/newgrouppage9.cfm?objectgroup_id=8862Thorlabs for Femo sell appropriate amplifiers.
We have developed one that works great. It's documented here: https://www.janelia.org/open-science/pmt-amplifier