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You should really have an IR blocking filter in the transmitted light 
path. I suspect the IR from the halogen lamp is fooling the PFS into 
thinking it's seeing the coverslip reflection when really it's just 
seeing the IR from the transmitted light. At least in our scopes, Nikon 
always puts an IR blocking filter in the transmitted light path to 
prevent these problems.

Kurt

On 2/28/2012 5:07 AM, Andrew Vaughan wrote:
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>
> Dear all,
>
> I wonder if anyone out there can help me with a problem I'm having with the
> Perfect Focus System on a Nikon Ti. Basically, the PFS won't work when I use
> my 100X VC Plan Apochromat objective. My specimens are in various vessels,
> but all of them have coverslip thickness glass and at least 3mm of
> water/medium. When I focus on a specimen the PFS focus indicator light on
> the front of the stand indicates that the objective lens is not in the focusable
> range, even when the objective is focussed on the very surface of the
> coverslip. To test this I drew crosses in fine black marker pen on the inner
> coverslip surface of various chamber types. I then filled the chambers with
> water and focussed on the cross using transmitted light. My results are as
> follows:
>
> 1. The failure of the PFS seems to be limited to the 100X VC Plan Apochromat.
> Lower power lenses have consistently worked when tested.
> 2. If I move the stage so that the entire field is filled with the dark marker
> pen, the focus indicator lights up and PFS works. This is true whether or not
> the transmitted light is on or switched off.
> 3. If I get the PFS to work in the manner above and then move the stage so
> that I’m looking at an area free of marker pen the PFS stays on unless I turn
> the transmitted light off or put an IR blocking filter in front of the transmitted
> light.
> 4. If I blindly (with the transmitted light off) move the stage back into an area
> where there is marker pen, the focus indicator light comes back on and the
> PFS will work.
> 5. Additionally, if I get the PFS working using the method above and then
> move the stage into a clear area – while still observing using transmitted light
> – and then try to adjust the offset using the PFS Offset Controller, this causes
> the PFS to fail again.
>
>  From this I can say certain things:
>
> 1. Only the 100X VC Plan Apochromat is affected
> 2. A dark field (or possibly one with high contrast edges) is required for the
> PFS to work initially
> 3. The PFS can be sustained by IR light coming from the halogen lamp, but
> this isn't enough to get it going initially
> 4. Adjusting the offset, which moves the dichroic mirror in the PFS nosepiece,
> seems to take the system out of the focusable range
>
> Note that I can’t rule out a fault with the objective, but I have compared this
> objective with another identical objective in other tests recently and have no
> reason to believe it is faulty.
>
> Any ideas or suggestions would be most welcome.
>
> Thanks,
>
> Andrew.
>