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pipeline:window:e2boxer

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pipeline:window:e2boxer [2018/06/20 13:12]
127.0.0.1 external edit
pipeline:window:e2boxer [2019/04/02 09:21]
lusnig
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 ===== Input ===== ===== Input =====
 === Main Parameters === === Main Parameters ===
-  ; input_micrograph_list : Input micrograph list: Wild cards (e.g. *) can be used to specify a list of micrographs. Not recommended if the number is very large. (default required string)+  ; 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)   ; %%--%%apix : Pixel size [A]: Angstroms per pixel for all images. (default -1)
   ; %%--%%boxsize : Box size [Pixels]: Box size in pixels. (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)   ; %%--%%ptclsize : Particle diameter [Pixels]: Longest axis of particle in pixels (diameter, not radius). (default -1)
-  ; %%--%%invert : Invert input contrast: If specifiedinverts input contrast. Particles MUST be white on a darker background. (default False)+  ; %%--%%invert : Invert input contrast: Preferablyparticles should be brigt on a dark background. (default False)
   ; %%--%%no_ctf : Disable CTF estimation: Disable CTF estimation. (default False)   ; %%--%%no_ctf : Disable CTF estimation: Disable CTF estimation. (default False)
   ; %%--%%gui : Interactive GUI mode: Use interactive GUI mode. (default False)   ; %%--%%gui : Interactive GUI mode: Use interactive GUI mode. (default False)
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 \\ \\
 === Advanced Parameters === === Advanced Parameters ===
-  ; %%--%%allmicrographs : Include all micrographs in a directory: Add all images from micrographs folder. (default False) 
   ; %%--%%unboxedonly : Include only unboxed micrographs: Only include image files without existing box locations. (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)   ; %%--%%write_ptcls : Save selected particle: Extract selected particles from micrographs and write to disk. (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 : 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)   ; %%--%%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)   ; %%--%%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)   ; %%--%%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)   ; %%--%%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, when multi-computer parallelism isn't useful. (default 4)+  ; %%--%%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)   ; %%--%%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)   ; %%--%%verbose : Use verbose mode: Specify verbose level [0-9]. Higner number means higher level of verboseness. (default 0)
pipeline/window/e2boxer.txt · Last modified: 2019/04/02 09:21 by lusnig