Scanning electron microscopes (SEM) are widely used to analyse the morphology of all kind of specimen providinghigh resolution image data. To overcome the two-dimensional limitation, a lot of effort has been put into the recovery ofthe hidden third dimension based on the acquired SEM images throughout the last decades. Especially methods based onphotogrammetry were identified to yield qualitatively good reconstruction results. Nevertheless, precise quantitative 3Dmeasurements still remain a challenge. One of the key problems is the robust estimation of the motion in the acquiredimage sequences. A possible solution is given by the factorization method for orthographic image streams. To evaluatethe applicability of this algorithm on SEM image sequences, the motion for several sequences is estimated and comparedto the stage settings. Furthermore, the method is extended to obtain a dense reconstruction from a stereo-pair based onthe estimated rotations between the two views. The final reconstruction results are compared to reference measurementswith a confocal laser scanning microscope for a quantitative evaluation.
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