search

scipion-em / scipion-em-imod

Plugin to use some of the Tomography tools from IMOD in Scipion
GNU General Public License v3.0
1 stars 2 forks source link

Imod tilt-series normalization is introducing some error in the alignment matrix #155

Open fede-pe opened 1 year ago

fede-pe commented 1 year ago

When binning a tilt series with a transformation matrix associated, it is necessary to correct the scale of the shifts in order to keep the alignment consistent.

azazellochg commented 1 year ago

I think this is already done : https://github.com/scipion-em/scipion-em-imod/blob/devel/imod/protocols/protocol_tsNormalization.py#L258

fede-pe commented 1 year ago

You are right. Let me check why it is failing to me then. The behavior I am experiencing is that when applying ts normalization before reconstruction the final tomogram appears artifacted. This only happens when taking the TS with the associated alignment info (if taking the interpolated tilt series for normalization then the tomogram seems to be correct).

pconesa commented 1 year ago

I think what is happening is that is applying the transformation matrix, but not removing it from the set.

I'd suggest to add a parameter to do it or not...and clear the matrix if apply?