Three-dimensional alignment of density maps in cryo-electron microscopy

Yael Harpaz, Yoel Shkolnisky

Research output: Contribution to journalArticlepeer-review


A common task in cryo-electron microscopy data processing is to compare three-dimensional density maps of macromolecules. In this paper, we propose an algorithm for aligning three-dimensional density maps, which exploits common lines between projection images of the maps. The algorithm is fully automatic and handles rotations, reflections (handedness), and translations between the maps. In addition, the algorithm is applicable to any type of molecular symmetry without requiring any information regarding the symmetry of the maps. We evaluate our alignment algorithm on publicly available density maps, demonstrating its accuracy and efficiency. The algorithm is available at
Original languageEnglish
Pages (from-to)e8-1 - e8-21
Number of pages22
JournalBiological Imaging
StatePublished - Mar 2023


  • Algorithms
  • Alignment
  • Cryo-electron microscopy
  • Cryogenic electron microscopy
  • Data processing
  • Electron microscope
  • Electron microscopy
  • Handedness
  • Macromolecules
  • Maps
  • Medical Sciences--Radiology And Nuclear Medicine
  • Microscopy
  • Molecular symmetry
  • Optimization
  • Software packages
  • Three-dimensional space
  • global map alignment
  • synchronization
  • three-dimensional alignment


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