We describe a novel and noninvasive, microscopy-based method for visualizing the structure and dynamics of microbial biofilms, individual fluorescent microbial cells, and inorganic colloids within a model porous medium. Biofilms growing in flow cells packed with granules of an amorphous fluoropolymer could be visualized as a consequence of refractive index matching between the solid fluoropolymer grains and the aqueous immersion medium. In conjunction with the capabilities of confocal microscopy for nondestructive optical sectioning, the use of amorphous fluoropolymers as a solid matrix permits observation of organisms and dynamic processes to a depth of 2 to 3 mm, whereas sediment biofilms growing in sand-filled flow cells can only be visualized in the region adjacent to the flow cell wall. This method differs fundamentally from other refractive index-matching applications in that optical transparency was achieved by matching a solid phase to water (and not vice versa), thereby permitting real-time microscopic studies of particulate-containing, lowrefractive-index media such as biological and chromatographic systems.

Lightguides were fabricated from three commercial polyimides of which one contains one and the others contain two hexafluoroisopropylidene (6F) groups. The latter are isomers using either the para or the meta isomer of the same diamine. As the number of 6F groups increases the optical losses of the corresponding lightguides decreases. In thick lightguides of the two 6F groups containing polyimides, loss values below 0.1 dB/cm can be realized using optimized conditions. Two mechanisms-ordering with or without charge transfer complex formation and voids or pinholes-are seen to be responsible for optical losses. The second type of losses can be reduced by cure optimization. Where ordering is possible annealing leads to increased optical losses. Geometrical restraint of the ordering, however, leads to loss reduction in otherwise identical conditions. Losses observed in the bulk are always higher than in the top and bottom layers of the polyimide films.

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