Leginon

Make movie stack with dark/bright/norm/gain references yourself without Leginon/Appion libraries¶

If you want to do everything yourself, you can use the python script

getReferences.py

to find the location and filenames of the bright, dark, norm (also known as gain) references and work on them yourself. The filenames are formatted to include various information. For example,

14aug12a_12221419_00_512x512_norm_0.mrc is a norm reference image at dimension of 512x512. It was calculated from the dark and bright images shown by the script and was taken during session 14aug12a at 22:14:19 and is for correction channel 0.

Beware that the fames are often in different orientation from the reference images in Leginon

To apply the correction, you need to use the equations found in Corrector

If there are no bad pixel/column/row on your camera that you included in your correction plan, you can feed the properly rotated/flipped references to the 2.0+ version of the drift correction program (motioncorr) by Xueming Li.

simple_correctstack.py can do the same as well using the library of Leginon/Appion, but not the database.