Bug #962
closedbeam tilt value from some version of tecnai or TEM scripting is not in radian
100%
use a larger beam tilt knowing that it is not in radian. The two scopes we saw this need a factor of 6.
Description
Some tecnai(TEM) scripting gives beamtilt value through Illumination.RotationCenter in radian. Some version gives it in some unknown unit. We do not know when the change occurs and if this is true for all versions after a certain time.
Here is one way to tell while using Leginon to calibrate defocus in Beam_Tilt node:
The default 0.01 radian beam tilt with -2 um defocus and -4 um defocus should separate by 20 nm in theory, assuming Cs=2.0 mm. This is equivalent to 100 pixel on a 2 Angstrom pixel-size CCD. For a 4kx4k camera, it means 1/40 of the length of image. If the correlation peak position during defocus calibration barely moved from the origin, your scope does not give radian value by this function call.
Updated by Anchi Cheng over 13 years ago
- Category set to Leginon subsystem
- Status changed from Assigned to In Code Review
- Assignee changed from Anchi Cheng to Jim Pulokas
- Priority changed from Normal to Immediate
- Target version set to Appion/Leginon 2.1.0
- % Done changed from 0 to 100
r14924 (trunk) and r14920 (2.1) set rotation_center_scale at the beginning of the file and use it to convert from radian to Ilumination.RotationCenter values.
r14923 (trunk) is a script for people to find the correct scale with a gold grating replica.
Updated by Jim Pulokas over 13 years ago
- Status changed from In Code Review to Closed
reviewed and tested.
Updated by Scott Stagg over 13 years ago
I just updated my pyscope to 2.1 and noticed this. Our Titan required a value of 6.0. I don't know if you are keeping track of this, but I thought you might like to know. I guess I have been getting around this unknowingly by increasing the beam tilts or something like that.
Updated by Anchi Cheng over 13 years ago
Thanks for new data point in the database. It is likely on all the newer versions for Tecnai and Titan scopes, then. We still can't be sure which version it started.