Preprocess images: Difference between revisions
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* Unmasked (masking is performed internally) | * Unmasked (masking is performed internally) | ||
* Non-interpolated (prevent any prior rotations/translations: use the originally scanned pixel values) | * Non-interpolated (prevent any prior rotations/translations: use the originally scanned pixel values) | ||
** If downscaling is necessary because of memory issues: use a window-operation in Fourier-space, not a convolution (e.g. with rectangle/B-spline). Xmipp implements the Fourier-space downscaling in the <code>xmipp_scale</code> program with the <code>-fourier</code> option. | ** If downscaling is necessary because of memory issues: use a window-operation in Fourier-space, not a convolution (e.g. with rectangle/B-spline). | ||
** Xmipp implements the Fourier-space downscaling in the <code>xmipp_scale</code> program with the <code>-fourier</code> option. | |||
* '''un'''corrected for | |||
RELION does not discard any image during refinement. Therefore, data sets should be clean from ''false'' particles. Masking and CTF correction are done internally, so in the preprocessing images do not need to be masked, nor CTF phase-flipped or Wiener-filtered. The images should be normalised, but the exact procedures do not matter much, as also normalisation errors may be corrected inside the refinement. | RELION does not discard any image during refinement. Therefore, data sets should be clean from ''false'' particles. Masking and CTF correction are done internally, so in the preprocessing images do not need to be masked, nor CTF phase-flipped or Wiener-filtered. The images should be normalised, but the exact procedures do not matter much, as also normalisation errors may be corrected inside the refinement. | ||
CTF phase-flipping | CTF phase-flipping | ||
Revision as of 20:45, 27 September 2011
RELION will work best if your data set is:
- Of high signal-to-noise ratio (take great care in sample preparation and data collection)
- Clean from false particles (no images are discarded during refinement).
- Xmipp implements a utility called
xmipp_sort_by_statisticsto sort particles which comes handy in the cleaning of a data set.
- Xmipp implements a utility called
- Unmasked (masking is performed internally)
- Non-interpolated (prevent any prior rotations/translations: use the originally scanned pixel values)
- If downscaling is necessary because of memory issues: use a window-operation in Fourier-space, not a convolution (e.g. with rectangle/B-spline).
- Xmipp implements the Fourier-space downscaling in the
xmipp_scaleprogram with the-fourieroption.
- uncorrected for
RELION does not discard any image during refinement. Therefore, data sets should be clean from false particles. Masking and CTF correction are done internally, so in the preprocessing images do not need to be masked, nor CTF phase-flipped or Wiener-filtered. The images should be normalised, but the exact procedures do not matter much, as also normalisation errors may be corrected inside the refinement.
CTF phase-flipping