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In electron microscope tomography, alignment of tilt series images is a major determinant of resolution in 3D reconstructions. One alignment method uses gold beads deposited on or in the specimen as fiducial markers. We have developed software called “xpix2” that picks markers semi-automatically. It uses a cross-correlation function to determine the shift between tilt images and predicts marker positions. Then it refines them in a local search area, and detects and corrects wrongly picked markers automatically. xpix2 checks its own status and pauses to ask the operator to intercede if it finds that most markers are wrongly picked. xpix2 is more accurate than manual picking. We now use this software in our research unit.

Xpix2: Software to Pick the Fiducial Markers Semi-Automatically in Electron Tomography Tilt Images