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stereo calibration

I have been using Matlab Calibration Toolbox to calibrate my stereo camera. The result is not satisfying. I extract salient features from both images and verify the calibration result based on rectification result. After rectification, the features in the same pair are misaligned by roughly 10 pixels in y axis. I would expect the rectification error in y axis to be around 1 pixel.

Following the Opencv calibration example, for some images, the software fails to detect all the corner. Can someone comment on this? Also I have attached sample left and right images taken for calibration.

C:\fakepath\left0.jpg C:\fakepath\right0.jpg