Directory Structure for 3D EM Image Processing
In a Typical Project Directory:
./Batch/
-batch procedures that have been executed for the project
./Micros/
-original scanned tif micrographs
-spider micrographs (usually binned by 3 or 4 during conversion)
-binned spider micrographs (usually binned an additional 4x for particle selection)
-list of micrographs (e.g. "microlist.spi"), 1st column is micro_number
-particle coordinates for each micro
-angles for each tilted micro
./PowerSpectra/
-2D power spectra ("pwavgs@****")
-1D rotationally averaged power spectra for fitting in Web ("pwdoc****")
-list of defocus values ("defocus")
./Particles/
-raw particles ("pcls@" or untilted = "pclu@" and tilted = "pclt")
-normalized particles ("npcls@")
-filtered particles ("fnpcls")
-masked particles ("mfnpcls")
./FreeAlign/
-alignment parameters ("alndoc" contains alpha, xshift, yshift)
-averages
./Classify/
-lists of classes
-lists of class memberships
-class averages
./RefAlign/
-alignment parameters ("apshdoc")
-averages
./RefAlign/BackProject/
-projection angles for tilted particles calculated from alignment parameters of untilted pair ("rctangles")
-refined 3d rct structures (e.g. "vol***")
This directory organization is compatible with my batch procedures that call my scripts library and SPIDER commands.