Leginon

h2. Make DDD movie stack

The following section comes from Appion Manual

{{include(appion:Direct_Detector_Frame_Processing)}}

h2. Making Gain/Dark correction one image at a time without saving results to databases

Two scripts are attached here.  They use Leginon infrastructure to locate references and do gain/dark correction and bad pixel/column/row correction.  It, however, does not involve saving results to the leginon/appion databases.  These are good for testing of add your own idea to it.

*correctframes.py* let you correct a range of raw frames in an image and output as mrc file.

*correctstack.py* let you correct each frame in the specified summed image and output at 2D image stack in mrc format.

type:

<pre>

python correctframes.py

</pre>

for the options

h2. [[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":http://emg.nysbc.org/projects/leginon/repository/changes/branches/myami-3.1/leginon/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_dark_0.mrc* is a dark reference image at dimension of 512x512.  It 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* attached here can do the same as well using the library of Leginon/Appion, but not the database.