Depends on your microscope and filter set-up. The emission spectra overlap a lot, but the FM1-43 emission peak extends substantially into the green spectrum, where LTR fluorescence is pretty much nil. If you can get the concentrations right to achieve a similiar signal intensity for both dyes, you could use a standard GFP/FITC filter cube for FM1-43 and a RFP/TRITC cube for LTR without too much crosstalk. Completely avoiding it would mean using more exotic excitation and emission wavelenghts, which will not be routinely available.
Other options (again depending on your filter set-up): LTBlue+FM1-43, LTGreen+FM4-64, LTBlue+FM4-64. None of them are perfect, unfortunately.
@Konstantin Thanks for the answer. Our setup is a TCS SP5 multiphoton laser scanning confocal microscope so its pretty "easy" to play with the excitation/emission wavelengths. We have tried different settings and even though LTR was set to 600/699 there is still considerable fluorescence at this setting when using FM1_43 alone. May try Lysotracker deep red.
Yes, FM 1-43 has a tendency to overpower most other dyes. LT Deep Red is probably your best bet, at 640nm FM1-43 excitation should be 0.
Btw, there's a reason LT Deep Red comes in brown tubes instead of clear ones: it bleaches quite rapidly compared to the other Lysotrackers. Good Luck!
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