1. The type entries indicate the kind of data expected to be in the field: one or two integers (separated by a comma), one or two floating point numbers, a boolean value of 0 or 1, or a text string. Text string entries marked as "File" will be shown with a file chooser button in the template editor in Etomo.
  2. Template directives must either specify absolute paths or have just a filename with no path. In the latter case, the files are sought in their default locations:
    • A scope template file is expected to be in $IMOD_CALIB_DIR/ScopeTemplate.
    • For a system template, the program looks in $IMOD_CALIB_DIR/SystemTemplate, and if the file is not there, it looks for it in $IMOD_DIR/SystemTemplate. Thus, a customized file placed in the IMOD_CALIB_DIR location will override a file of the same name distributed with IMOD.
    • A user template file is expected to be in the user's selected template directory, which is $HOME/.etomotemplate by default and can be changed in the Settings dialog in Etomo.
  3. Template and batch directive filenames must end in the extension ".adoc".
  4. Rules for the treatment of directives and the format of values are described in the man page for Batchruntomo. Some essentials are:
  5. Directives marked with Y in the Tmplt column can be included in a template file. These and all other directives have an effect when the relevant step is run by Batchruntomo. The entry in the Etomo column determines whether they have an effect when running the relevant step for the first time in Etomo as well as the behavior of the directive editor.
  6. The entry in the Etomo column has these meanings:
  7. "BRT default" refers to a default value applied by Batchruntomo. "Etomo batch default" refers to a default value that the Etomo batch interface obtains from IMOD/com/batchDefaults.adoc.
  8. Directives to run a command in place of or after a given step have these rules: