You should be able to do this with a sample player that fully supports VST3 (but not with one which only supports VST2). If you are playing polyphonic notes on one MIDI channel, VST3 allows you to "pitch-bend" each note independently, unlike VST2 which only allows pitch-bend commands to affect all notes being played on a MIDI channel.
You might want to look at the trial version of Dorico, which should be able to use this capability direct from music notation written using microtonal accidentals, with its bundled sound samples. You can define customised microtonal intonation systems, if you want to use something more exotic than "standard" microtonal notation like quarter-tones.
Using this technology for live performance brings in another set of challenges of course, unless you have a MIDI keyboard with more than 12 keys per octave!