the composition of the membrane matter too. I think PET (polyester) membranes are better than polycarbonate or PTFE because they let the light go through.

 Thanks! They are porcine intestinal epithelial cells. I use collagen-coated PTFE inserts (they are supposed to be suitable for immunofluorescence).

Maria, 

You could opt for clear transwell inserts that will be helpful for microscopy. I tried live confocal imaging using transwell inserts, but was not successful. Best way is to cut the membrane after fixing the cells and invert it on the coverslip and mount. 

https://www.researchgate.net/post/Can_transwell-cultured_Caco-2_monolayers_be_imaged_using_spinning_disk_confocal_microscopy2

Thanks a lot for your all your suggestions!

I will be coculturing epithelial cells on the top surface of the transwell insert and endothelial cells on the bottom surface of the insert. I was wondering how to image the membrane after I fix and stain the cells. Please suggest me the best way to mount the membranes and what is the best mounting medium for this purpose. I will be using 6.5mm PET inserts.