Wrong alignment after re extraction

[olibclarke]

What CS version are you using?

Wondering if the downsampling in your workflow may be causing the issue:

Recentering when downsampling does not update particle locations

When using the “Downsample particles” job with the “Recenter using aligned shifts” setting enabled, the resultant .cs file shows that the alignment shifts are reset to sub-pixel values (presumably to match the new images), but the particle coordinates/locations are not updated. Thus if these are later re-extracted, or the original particle.blobs are attached, they reconstruct with the original centre but with loss of aligned shifts, resulting in a poorly aligned average. This is particularly ap…