Leginon

h2. Make DDD movie stack

The following section comes from Appion Manual

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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. Do it yourself

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 references and work on them yourself.

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

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 drift correction program by Xueming Li.