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Automatic Tilt Series Alignment for Improved 3D Reconstruction in Electron Microscopy

This study presents an approach for automatic alignment of tilt series using the Xmipp software, streamlining the process of 3D reconstruction in electron microscopy. The method eliminates the need for gold particles by utilizing automatically detected landmark chains and estimating affine transformations to track critical points across images. Our results demonstrate the efficiency of the technique, with significant improvements in processing time and accuracy. With the potential for batch mode reconstruction applicable to various imaging techniques, this method marks a significant advancement in the field.

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Automatic Tilt Series Alignment for Improved 3D Reconstruction in Electron Microscopy

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  1. Automatic tilt series alignment C.O.S. Sorzano, C. Messaoudi, M. Eibauer, R. Hegerl, R. Marabini, S. Nickell, S. Marco, J.M. Carazo. Biocomputing Unit, National Center of Biotechnology (CSIC), Spain Max-Planck Institute for Biophysics, Germany Institute Curie, France

  2. Problem statement

  3. Manual alignment IMOD

  4. Manual alignment IMOD

  5. Choose landmark chains Estimate 3D landmarks and tilt axis Discard wrong chains Automatic image alignment xmipp_angular_assign_for_tilt_series

  6. Automatic image alignment xmipp_angular_assign_for_tilt_series • Choose landmark chains • Estimate affine transformations between image pairs • Track small local regions along the tilt series as much as possible (use the affine transformation as first approximation and locally refine through correlation) No need for gold particles!!

  7. Automatic image alignment xmipp_angular_assign_for_tilt_series • Choose landmark chains • Estimate affine transformations between image pairs • Track critical points (local minima after noise supression)

  8. Automatic image alignment xmipp_angular_assign_for_tilt_series • Choose landmark chains • Estimate 3D landmarks and tilt axis Iterative solution • Discard wrong chains • Discard through residuals

  9. Results Slices through the automatically reconstructed volume Slices through the manually reconstructed volume

  10. Performance 8 processors: • 512x512x91= 10 minutes • 650x650x121= 15 minutes • 1300x1300x121= 2 hours Reprojection error between 0.5 and 1.5 pixels

  11. Availability

  12. Availability: Xmipp and TomoJ

  13. Conclusions • Tilt series alignment can be achieved by many short automatically detected chains • Many is between 500 and 10.000 • Short is: • Grid: between 5 to 20 images • Critical points: between 10 to 30 images • Few parameters: • Grid: correlation threshold between patches • Critical points: number of seeds in each image • Fast depending on size • The absolute position of the tilt axis cannot be uniquely determined by the projection geometry • Future: Batch mode reconstruction (X-rays, EM)

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