Most exciter and emitter filters have an arrow on the aluminum housing.  Filters should be oriented so that the arrow points in the direction of light propagation – from the light source to the dichroic for the exciter and from the dichroic to eye or camera for the emitter. The dichroic should be oriented such that the reflective coating side faces toward the exciter or light source and the sample, as shown in the diagram below. 

For standard catalog dichroics, the reflective side is marked with the Semrock logo and part number or scribe as shown in the example at right.

For further details on filter orientation, please review the technical note: Orientation of Filters in a Microscope.

Complete how-to instructions for microscope cube assembly are available in PDF format and video.