Make DDD movie stack¶

The following section comes from Appion Manual

Direct Detector Frame Processing¶

This section enables the user to create gain/dark corrected frame stack in mrc format from raw movie frames generated by direct detectors such as Direct Electron DE12 or DE20, Gatan K2 Summit. The equation used is found in this wiki on corrector

FEI Falcon II "raw" frames are already gain/dark corrected. The frame stack making process does not do that. However, it compiles the individual images as standard 32-bit float mrc image stack in this process and perform drift correction if so requested.

Gain/Dark Correction of movie frames¶

1. makeDDRawFrameStack: Frames obtained from DD, except Falcon, are not yet corrected for variation of pixel response. In the case of analog detection such as those performed by DE series and K2 Linear mode, they are also not dark corrected. This process performs these correction. The output is 32-bit mrc image stack. Also, it can be followed by frame alignment.
2. Catch up DD frame alignment: Using defergpu option in makeDDRawFrameStack when aligning, the gain/dark correction and alignment are broken up for more efficient use of gpu-capable host. In such a case, this process is launched.

Appion SideBar Snapshot:¶

Notes, Comments, and Suggestions:¶

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^ Appion Processing

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Run one image at a time without uploading aligned to Leginon/Appion databases¶

Two scripts not involving saving results to the leginon/appion databases are attached here

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:

python correctframes.py

for the options

Do it yourself¶

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

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