The first step in the measurement process using the Handy PEA chlorophyll fluorimeter is to cover the sample area to be analysed, with a small, lightweight leafclip. The clip has a small shutter plate which should be closed over the leaf when the clip is attached so that light is excluded and dark adaptation takes place. The body of the clips are constructed from white plastic to minimise the effects of heat build-up on the leaf during the period when the clip is in place. The locating ring section of the clip which interfaces with the fluorimeter optical assembly is constructed from black plastic. This ensures that the measurement is unaffected when measuring during conditions of high ambient light intensity.

The leaf or needle rests on a foam pad whilst in the clip in order to minimise damage to the structure of the leaf. The shutter plate should be closed to exclude light from the sample during dark adaptation.

During dark adaptation, all the reaction centres are fully oxidised and available for photochemistry and any chlorophyll fluorescence yield is quenched. This process takes a variable amount of time and depends upon plant species, light history prior to the dark transition and whether or not the plant is stressed. Typically, 15 - 20 minutes may be required to dark adapt effectively. In order to reduce waiting time before measurement, a number of leaves may be dark adapted simultaneously using several leafclips. Some users even make measurements at night, thus ensuring an adequate supply of readily dark adapted samples and zero waiting time!