fiji/Correct_3D_Drift

Unable to apply pre-computed vectors

Opened this issue · 4 comments

DSbioimaging commented

Thank you for the tool, I was unable to find a way (either in FIJI forum searches or the documentation) to apply the pre-computed vectors, is there an intended way to do it?

tischi commented

Hi, could you please elaborate what you mean by "pre-computed vectors"?

One can apply transformation txt files created with elastix.

DSbioimaging commented

The plugin has a checkbox called "Only compute drift vectors?" which results in an a text file containing the translation shifts between slices and time points, similar to what Elastix produces.
I wondered whether there was an intended way to apply these pre-computed shifts to other data without performing further computations (e.g. applying a transformation file in Transformix).

tischi commented

I see, sorry, no, I don't have anything for that.
To be honest also don't have time to add it.
Would you like to add it? :-)

tischi commented

I think it will be tricky though, because it would make the current user interface even more complex...
Maybe one would need a second script.
This is the first one: https://github.com/fiji/Correct_3D_Drift/blob/master/src/main/resources/scripts/Plugins/Registration/Correct_3D_drift.py