The job 'AlignTiltSeries' in RELION 5.0.x can work with IMOD or AreTomo2.
The first page includes "Estimated tomograms thickness (nm): 300 - default", which might be used to create an -AlignZ value for AreTomo2.
It looks like the math here is 300nm / pixel size * 10A / nm = -AlignZ value provided for AreTomo2. The issue is that these default values appear quite large for AreTomo2 and lead to bad alignment performances, rather having a much smaller 1/3 the total estimated tomograms Z height will often give much better aligned stack.
The help is "Estimated tomogram thickness (in nm) to be used for projection matching in AreTomo2 and for patch tracking in IMOD", it is easy to get tripped up here - see other issue #1168. It would be better to rename this field as "Alignment Z-Height" rather than "Estimated tomograms thickness" and indicate in the ? help that this will be used to determine the pixel height of -AlignZ.
Another related request, can patch tracking options (-patch X Y) be exposed in the AreTomo wrapper?
Thanks,
Matt
The job 'AlignTiltSeries' in RELION 5.0.x can work with IMOD or AreTomo2.
The first page includes "Estimated tomograms thickness (nm): 300 - default", which might be used to create an -AlignZ value for AreTomo2.
It looks like the math here is 300nm / pixel size * 10A / nm = -AlignZ value provided for AreTomo2. The issue is that these default values appear quite large for AreTomo2 and lead to bad alignment performances, rather having a much smaller 1/3 the total estimated tomograms Z height will often give much better aligned stack.
The help is "Estimated tomogram thickness (in nm) to be used for projection matching in AreTomo2 and for patch tracking in IMOD", it is easy to get tripped up here - see other issue #1168. It would be better to rename this field as "Alignment Z-Height" rather than "Estimated tomograms thickness" and indicate in the ? help that this will be used to determine the pixel height of -AlignZ.
Another related request, can patch tracking options (-patch X Y) be exposed in the AreTomo wrapper?
Thanks,
Matt