Appion

h1. Typical Appion workflow package requirement of Appion scripts

Appion python scripts are often wrappers that calls scripts or command from other packages.  List here are what is needed by each typically used options. Note that users may not want to use all functions as programs go out of fashion.

h2. Direct Detector Frame Alignment

|appion script name|subfunction|external package|script/command within the package|

||general image manipulation||EMAN1|proc2d|

|makeDDAlignMotionCor2_UCSF.py||MotionCor2|

|makeDDAlignMotionCorr_Purdue.py||motioncorr v2.0 from Purdue|

|makeDEAlignedSum.py||deProcessFrames.py||

|makeDEAlignedSum.py||EMAN2||

h2. Automated CTF Estimation

|appion script name|external package|

|ctffind4.py||CTFFIND4|

|gctf.py|Gctf|

h2. Particle Selection

|templateCorrelator.py|template-based particle selection|FindEM|

|gAutomatchFast.py|template-based particle selection|Gautomatch|

h2. Particle Stack Making and manipulation

|makestack2.py|making Imagic stack|appionlib||

|makestack2.py|making Relion stack|Relion|relion_preprocess or relion_preprocess_mpi|

|makestack2.py|CTF correction by Wiener filtering of the full image (Imagic stack only)|ace2|ace2correct.exe|

|makestack2.py|normalization by edge|appionlib||

|makestack2.py/quickstack.py|making montage of stack mean/standard deviation map|ImageMagick|montage|

|centerParticleStack.py|particle centering in a stack|EMAN1|centeralignint|

|boxMaskStack.py|soft masking of helical boxed particles in the stack|Spider|