Chips can be assembled “trench-up” or “trench-down”. The trench is part of the thick silicon support for the porous membrane.
Chip Orientation – Video of Rotating Chip
For cell culturing, cells can be cultured on the flat membrane side and on the trench side, depending on the application. When imaging, you will be able to see both cells through the porous membrane portion. When fluorescently labeled, you will also be able to see the cells on the side of the thick silicon substrate that faces the light source.
In a coculture, you can visualize cells on the side towards the light source. In a trench-down device, the cells cultured in the trench (red) can be seen along edges (see arrows), albeit blurry because they are out of focus. The cells cultured on the opposite side (green) can only be seen in the window.
Below is another example of visualizing cells cultured on the side of the light source (top) versus opposite of the light source (bottom).
Finally, these are images of the same cell monolayer. In the top image, cells are on the opposite side of the light source and can only be seen in the transparent region. In the bottom image, the chip has been inverted, and we can now see that cells are also growing outside of the transparent membrane region.