Firstly optimum Tim depending on the plant type . generally, when it in merstimatic case or phase . or just it has a complete structured and before opening

First you need determine the time in dark  that you plant tissue don´t have more excited electrons and make a curve , then when you determine the time appropiate, you can mantain in dark your tisssue (time depends of the curve) and obtain the real answer at light of fluorometer.

Hansatech fluorescence measurement system is basically used for chlorophyll fluorescence measurements of field/ pot grown plants. I never come across measuring fluorescence in in vitro plants. In field, fluorescence is measured during day time (10 to 11 h) either in dark-adapted leaves or without dark-adaptation as per the requirement of the study, to test the stress levels. Under in vitro conditions, plants are grown inside the culture room with optimum nutrient inputs & moisture in the medium with adequate artificial lights. Better to do the experiment in the field with the same plants that are grown under in vitro.   

Good luck