I am working with Turtlebots and ROS, and using a camera to find the pixel positions of a marker in the camera. I've moved over from simulations to a physical system. The issue I'm having is that the measured pixel positions in my physical system did not match the pixel positions in the physical system despite the marker and everything else being in the same position as in the simulations. The transforms between the camera and the marker were the same in both the simulations and the physical setup, meaning the same height difference and distance between the camera and object. Everything except for the camera (simulation using the default TB3 Waffle Pi camera and physical setup using Logitech C900 USB cam) and camera calibration matrices are the same. I've also made sure that there is no tilt in the camera and that it is pointing straight forward.

The camera calibration for the simulated system is ideal, the camera calibration for the physical system has bad camera calibration. The resolution I'm using is 640x480, so the center pixels should be cx=320 and cy=240, but what I noticed in the camera calibration matrix I was using in the physical system was that the cx was around 318, which is pretty accurate, but the cy was around 202, which is far from what it should be. This also made me think that the shift in pixel positions in the vertical direction is because of the camera calibration.

So my question is, does the calibration of the camera affect the pixel coordinates? Would two cameras with different calibrations detect the pixels in different coordinates, despite everything else (distance between camera and object, height between optical axis and object, etc) being the same? And would the same camera detect the pixel coordinates differently with different calibrations?