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I apologize for taking so long to respond to your worthy question. This thread got lost in the shuffle somehow.
The Y16 format shows only unrectified images and is to be used only when calibrating the camera. Do not use Y16 format in your applications.
Use Y8 format in your applications. The Y8 format provides rectified images. This means that the depth images captured by each depth sensor have been rotated to align with each other so that the rotation matrix in the extrinsics is the identity matrix.
Intel Customer Support