Feature #5972: add gui for editing image-shift coma and other related beam tilt calibrations - Leginon - Electron Microscopy Group

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Feature #5972

closed

add gui for editing image-shift coma and other related beam tilt calibrations

Added by Anchi Cheng about 6 years ago. Updated over 5 years ago.

Status:

Closed

Priority:

Normal

Assignee:

Anchi Cheng

Category:

Target version:

Appion - Appion/Leginon 3.4

Start date:

08/29/2018

Due date:

% Done:

Estimated time:

Deliverable:

Description

Currently, the calibration within leginon is not good enough but can be done with AutoCTF from Thermo Fisher. This feature allows those results to be enterred directly.

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Updated by Anchi Cheng about 6 years ago

Beam tilt unit is radians.
Beam-image shift (Known as image shift in leginon calibration) is in meters.
Read the beam tilt, stig, and defocus values from Scope EM node by refreshing its displayed values after AutoCTF make coma, stig and defocus correction.

BT_X(IS_X,0) = x axis beam-tilt required to bring image shift of (X, 0)
BT_Y(IS_X,0) = y axis beam-tilt required to bring image shift of (X, 0)
slope(BT_X(IS_X,0)) = the slope of a line fitting a series of BT_X at different (IS_X,0)

image-shift coma = [[ -slope(BT_X(IS_X,0)), -slope(BT_X(0, IS_Y)],
                      -slope(BT_Y(IS_X,0)), -slope(BT_Y(0,IS_Y)]]

image-shift stig = [[ -slope(Stig_X(IS_X,0)), -slope(Stig_X(0, IS_Y)],
                      -slope(Stig_Y(IS_X,0)), -slope(Stig_Y(0,IS_Y)]]

image-shift defocus = [[ -slope(Defocus(IS_X,0)), -slope(Defocus(0, IS_Y)],
                         1,                               1             ]]

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