Point Cloud Topology
The point cloud acquired by PhoXi 3D Scanner is topographically organized according to the image sensor. The photo from the image sensor is the texture image. For each pixel in the 2D sensor there is one computed 3D point. For the pixel that has "no 3D point" (because the area seen by this was not illuminated by the projection, usually due to the shadows) there is actually a "zero 3D point" = point at (0,0,0).
For example, the pixel at position [x= 2010, y =350] in the texture is the (2064*349 + 2010) = 722346-th point in the point cloud.
Unorganized point cloud
In the PhoXi Control, there is also an option to save the point cloud in PLY as "unorganized".
In unorganized point clouds the "zero points" are omitted and not saved. Therefore the topology is lost. You will need to use the depth map image to know which points are zero points and were skipped.