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.

You will also find reference images from correction channel 1 in the same folder with name like 14aug12a_12221421_00_512x512_norm_1.mrc which you may either ignore or use it in one of the two ways:
1. Create an average image with the one from correction channel 0 to get a reference image with better statistics ( i.e., 2n sampling of the population rather than n ).
2. Alternate its usage with the channel 0 result if your custom alignment program compares individual frames against each other, similar to the way Leginon use it for improving correlation peak with week signal.

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

Leginon/Appion 3.2 and up¶

For Leginon 3.2 and up, a references folder is created in the folder containing the raw frames. Inside the folder are

file	contents
reference_list.txt	gain/dark/defect/rotation/flip information for each frame stack
*norm_0.mrc	gain references as used in Leginon orientation
*dark_0.mrc	dark references as used in Leginon orientation before scaling to frame time
*norm_0_mod.mrc	gain references modified according to flip and rotation specified in reference_list.txt so that it can be applied directly to single frame
*dark_0_mod.mrc	dark references modified according to flip, rotation, and frame time specified in reference_list.txt so that it can be applied directly to single frame
defect_plan*.txt	defect rows, columns, pixels, respectively
defect_plan*_mod.txt	defect rows, columns, pixels, respectively, after flip/rotation modification to work with the frames

How to do the correction:¶

To apply the gain/dark 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 (*_mod.mrc) 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.

To apply defect correction, you will have to write an algorithm similar to what is in leginon correctorclient.py to find a good pixel not in the plan but closest to the defect as a substitution for the defected value.