Particle Coordinates (NEW): Generate files containing particle coordinates for all input micrographs by picking particles manual and/or automatically.

Usage in command line

e2boxer.py  input_micrograph_list  --apix=PIXEL_SIZE  --boxsize=BOX_SIZE  --ptclsize=PARTICLE_DIAMETER  --invert  --no_ctf  --gui  --write_dbbox  --allmicrographs  --unboxedonly  --write_ptcls  --suffix=SUFFIX  --voltage=VOLTAGE  --cs=CS  --ac=AMP_CONTRAST  --autopick=MODE  --threads=THREADS  --ppid=PPID  --verbose=LEVEL

e2boxer exists in non-MPI version.

Step 1: Use this command to start e2boxer's GUI with a list of micrographs using the right settings.

e2boxer.py CorrectedSums/corrsum_dose_filtered/*.mrc --apix=1.14 --boxsize=352 --invert --no_ctf --gui

Step 2: After user finished picking, run this command line to export .box files.

e2boxer.py CorrectedSums/corrsum_dose_filtered/*.mrc --apix=1.14 --boxsize=352 --invert --no_ctf --write_dbbox

input_micrograph_list

Input micrograph list: Wild cards (e.g. *) can be used to specify a list of micrographs. Not recommended if their number is very large. (default required string)

--apix

Pixel size [A]: Angstroms per pixel for all images. (default -1)

--boxsize

Box size [Pixels]: Box size in pixels. (default -1)

--ptclsize

Particle diameter [Pixels]: Longest axis of particle in pixels (diameter, not radius). (default -1)

--invert

Invert input contrast: Preferably, particles should be brigt on a dark background. (default False)

--no_ctf

Disable CTF estimation: Disable CTF estimation. (default False)

--gui

Interactive GUI mode: Use interactive GUI mode. (default False)

--write_dbbox

Export EMAN1 box files: Export EMAN1 box files (.box extension). (default False)

--unboxedonly

Include only unboxed micrographs: Only include image files without existing box locations. (default False)

--write_ptcls

Save selected particle: Extract selected particles from micrographs and write to disk. (default False)

--allmicrographs

Include all micrographs in a directory: Add all images from micrographs folder. (default False)

--suffix

Micrograph suffix: Suffix of the micrographs used for particle picking (i.e. suffix=goodali will use micrographs end with _goodali.hdf). It is only useful when –allmicrographs option is True. (default none): --allmicrographs==True

--voltage

Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. (default -1)

--cs

Microscope spherical aberration (Cs) [mm]: The spherical aberration (Cs) of microscope used for imaging. (default -1)

--ac

Amplitude contrast [%]: The typical amplitude contrast is in the range of 7% - 14%. The value mainly depends on the thickness of the ice embedding the particles. (default 10.0)

--autopick

Perform automatic particle picking: Provide mode and parameter string (eg - auto_local:threshold=5.5). (default none)

--threads

Number of threads: Number of threads to run in parallel on a single computer. (default 4)

--ppid

Parent process PID: Set the PID of the parent process, used for cross platform PPID. (default -1)

--verbose

Use verbose mode: Specify verbose level [0-9]. Higner number means higher level of verboseness. (default 0)

EMAN2 Group

Category 1:: APPLICATIONS

programs/e2boxer.py

Particle Picking with Convolution Neural Network

Beta:: Under development