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A multi photon microscope is a Fluorescence Microscope in which more than one Excitation Photons are used to excite the fluorophores.

How to treat 2-photon data in Huygens

Mind that the multi-photon option in a License String doesn't activate a new Microscope Type : the number of photons involved in the fluorescence process is a Microscopic Parameter that you have to enter when describing the image. The microscope type remains most of the times simply "widefield", but see below.

For 2-photon microscopes, the Excitation Photons parameter must be set to two.

Very large or no pinhole

If there is a non-descanned detector (NDD), or a very large (say > 10 Airy Disks ) pinhole, the contribution of the pinhole to the image formation can be ignored. In this case the microscope type can be set to Wide Field Microscope . This will result in more realistic values for the Nyquist rate than a confocal setting.

Fairly large pinhole

If there is a pinhole in the order of a couple of Airy Disks , typically 500 nm Back Projected radius, it must be taken into account. So in this case the microscope type type should be set to confocal, and the right Back Projected Pinhole Radius specified.

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