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I suspect that the problem is that you are saving your images as JPEG, and as far as I can remember it cannot handle 16 bit resolution. You can solve that by saving in PNG or TIFF.

Depth information is in the least significant 11 bits of the data, so you will see a dark image when you visualize it. Try normalizing or equalizing histogram; anyway remember that the information is still there, even if you can't see it. Some programs that can edit 16 bit images are Krita and Gimp (only lastest versions).

If useful, here is a ROS Indigo node that saves depth and color images from a Turtlebot's Kinect. Useful code is in guardar_imagenes.cpp