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From what I gather, you have obtained the Fundamental matrix through some means of calibration? Either way, with the fundamental matrix (or the calibration rig itself) you can obtain the pose difference via decomposition of the Essential matrix. Once you have that, you can use matched feature points (using a feature extractor and descriptor like SURF, BRISK, ...) to identify which points in one image belong to the same object point as another feature point in the other image.
With that information, you should be able to triangulate away.
