Expert Options of UNBLUR


I was wondering if there is any further reading for the expert options that are used during full-frame motion correction . I would like to understand the definitions
of these options as I am new to using Unblur

Joshua Lobo

Hi Joshua,

There isn't any proper documentation sorry. If you answer ? when it asks for a question, it will print a very short description which isn't much help. In general, you shouldn't need to set the expert options, if you want to play around with them - here is what they do (briefly), if you have any questions or need more detail please do ask.

Output FRC File - this is a text file which contains the FRC between the two half sums after alignment. In theory better FRC should mean better alignment, but it isn't all that reliable. For example, if you put all the shifts to 0, you will probably get the best FRC due to the detector artifacts adding up.

Minimum shift for initial search - this is the minimum shift allowed for the first round of alignment. This is used to force the frames to move in the first round so the next frame average doesn't just reinforce the detector artifacts.

Outer radius shift limit (Angstroms) - this is the maximum a frame is allowed to shift in any one round of alignment. You want this limited to limit the size of the search space, and thus limit the chances of a getting a spurious peak.

B-factor to apply to images - the reference has this b-factor applied, low pass filtering removes a lot of noise and detector artifacts

Half-width of central vertical/horizontal line of Fourier mask - the central cross in Fourier space is masked out up to this width, this is done as a lot of the power from detector artifacts is concentrated in these lines.

Termination shift threshold - this is the amount all frames must shift less than in a round before the alignment is stopped.

Maximum number of iterations - Max number of alignments that will be performed.