etomo(1)                    General Commands Manual                   etomo(1)

       etomo - A GUI program to run IMOD and PEET batch programs

       etomo [option ...] [data_file ...]

       ETomo is an interface for running a subset of IMOD and PEET commands.
       It can be run interactively, with automation, or with a combination of
       the two.  ETomo contains interfaces for a variety of projects:
       tomographic reconstructions, joining tomograms, subvolume averaging,
       aligning serial sections, blending montages, nonlinear anisotropic
       diffusion, running processes using IMOD's parallel processing
       capabilies, flattening tomograms, and testing a GPU.

       Automating Etomo functionality can be done with Etomo parameters and/or
       directives. For more information on directives, run imodhelp and choose
       "Directives for batch processing and Etomo templates" on the IMOD Help
       Index page.

       --h OR --help
              Output usage message.

              Forces all 3dmods to be run with the -L option.  This only has
              an effect on Windows computers because -L is always used on
              Linux and Mac.

              Moves the B axis window to the left of the A axis window when a
              major resizing event occurs.

       --namingstyle   0|1|2
              Sets the file name style for a new dataset.  Overrides the
              IMOD_OUTPUT_FORMAT environment variable for file name style
              only.  This does not affect the file format - just the file
              names.  0: the old non-standard file name.  1:the standard mrc
              extension.  2:The standard hdf extension.

              Send timestamps to standard error before and after processes are

       --userTemplateLoc    "directory_path"
              Adds a second User Template directory, in addition to one set in
              the Settings dialog.

       --directive     "directive_file.adoc"
              Causes automation to be performed based on a file called
              directive_file.adoc.  No interface will come up and some
              command-line automation options will have no effect.
              Command-line automation options that can be used with these
              These options are automatically set to true when --directive is
              The directive file must end in ".adoc" and conform to autodoc

              Used when batchruntomo calls Etomo.  Prevents Etomo from calling
              batchruntomo for validation.  Not used for calling Etomo from
              the command line.  When this option is used values from
              batchDefaults.adoc will be used in addition to any templates
              that are set.

       --axis     single|dual
              Sets the Axis Type in the Setup Tomogram dialog during

       --cpus     [ignored]
              Turns on the Parallel Processing checkbox in the Setup Tomogram

              Runs Create Com Scripts in the Setup Tomogram dialog during

       --dataset       tilt_series_file
              Deprecated.  Same as rawimagestack.

       --rawimagestack      tilt_series_file
              Sets Raw Image Stack in the Setup Tomogram dialog during
              automation.  The value should be set to a file containing a tilt
              series.  The file must be in the local directory unless a file
              path is included or the --dir option is used.

       --dir      "directory_path"
              For automation.  The absolute or relative directory containing
              the file or dataset specified with the --dataset option.

       --exit During automation, exit after the Setup Tomogram dialog has

       --fg   Causes Etomo to be run in the foreground rather then in the
              background.  This is useful when running Etomo with automation
              from a script because a script will not wait until a background
              command has completed.

       --fiducial      Floating point
              Sets the Fiducial Diameter in the Setup Tomogram dialog during

       --frame    single|montage
              Sets the Frame Type in the Setup Tomogram dialog during

       --gpus     [ignored]
              Selects the Graphics Card Processing checkbox in the Setup
              Tomogram dialog.

       --scan Runs Scan Header in the Setup Tomogram dialog during automation.

              For loading built-in plugins.  Will be expanded as necessary.
              Currently causes the etomo.plugin.demo package to be loaded in
              preference to external plugins implementing the same interface.

              Send actions and file name to Etomo's _err.log.  File names
              which do not contain an extension or are entirely numeric will
              be excluded.

       --debug    [-1|0|1|2|3|4]
              Send extra information to Etomo's _err.log.
              The optional parameter has the following meaning:
                -1 - limited output
                 0 - no debug output
                 1 - default debug output
                 2 - more information
                 3 - extensive information - log will be very large
                 4 - may degrade performance

       --grabit   [c|p]
              Grabit causes etomo to run as a command line program.  The
              purpose of grabit is to allow specific elements of etomo
              functionality to be tried out.  Currently it can only try out
              message processing so its possible that the parameters will
              change in the future.  When grabit is used the file names at the
              end of the command line will be assumed to contain program
              output file(s) to be processed by etomo's message processor.
              The result will be printed out.  Etomo will exit after doing
              this.  The parameter is optional.  Without a parameter it will
              create a generic message processor default settings.
              Optional Parameter:
                 b - batchruntomo but with logging off - has a special error
                 c - copytomocoms - multi-line warning and info messages
                 p - parallel processing with no multi-line messages

              ETomo will not load from or save to the .etomo configuration

       --memory   [interval_in_minutes]
              Send memory usage statements to Etomo's _err.log before and
              after processes are run.  nterval_in_minutes is the interval at
              which to send additional memory usage statements.

              Causes Etomo to do some internal testing. ETomo may run more

              Instead of popping up a message asking to close an open 3dmod
              instance, Etomo automatically closes it.  Used for automated
              user interface testing.

              No interface will come up.  Used for unit testing.

              The interface will come up in the default location rather then
              the location saved in .etomo.  Used for automated user interface

              The names of screen elements are sent to Etomo's _out.log.  Used
              for automated user interface testing.

              May cause Etomo to run with unreleased functionality.

       --test Used for unit testing and automated user interface testing.

       --demo Deprecated

   Data Files
              Tomographic reconstruction data file.

              Data file for joining tomograms.

              Subvolume averaging (PEET) data file.

              Data file for generic parallel process and nonlinear anisotropic
              diffusion interfaces.

              Data file for aligning serial sections and blending montages.

   Log Files
              Contains the log. The location is configurable (see man

              Contains the location of the log.  Placed in the directory from
              which Etomo is run.

              Contains the output of the --names parameter.  May also contain
              diagnostic messages.  Placed in the directory from which Etomo
              is run.

       Sue Held

       imodenv, uitest, 3dmod, imodhelp(1).

IMOD                               2/12/2009                          etomo(1)