PathViewer Command Line Tools

PathViewer 3.2+

Channel group import and export

omero pathviewer channelgroup get <object> [file]

Export image channel group settings

Positional Arguments:

  • object: Image selector, e.g. Image:123

  • file: File to write to. Default to standard output if not specified

omero pathviewer channelgroup set <object> [file]

Import image channel group settings

Positional Arguments:

  • object: Image selector, e.g. Image:123

  • file: File to read from. Default to standard input if not specified

Channel group settings are stored in JSON format and can be modified using an appropriate editor if desired.

PathViewer 3.3.5+

Fix invalid shape annotations

omero pathviewer maint fix_shape_annotations [--dryrun]

PathViewer versions 3.3.0 to 3.3.4 may have created invalid shape annotations in the database that can be corrected using this command. Use the optional --dryrun argument to find invalid annotations without fixing them.

PathViewer 3.4.0+

Label group import and export

omero pathviewer labelgroup list <object> [file]

List image label groups for ROI

Positional Arguments:

  • object: ROI selector, e.g. 123

omero pathviewer labelgroup get <object> [file]

Export ROI label group settings

Positional Arguments:

  • object: ROI selector, e.g. 123

  • annotation: Annotation identifier, e.g. 123. Omit to use default annotation

  • file: File to write to. Default to standard output if not specified

omero pathviewer labelgroup set <object> [file] [options]

Import ROI label group settings

Positional Arguments:

  • object: ROI selector, e.g. 123

  • annotation: Annotation identifier, e.g. 123, to overwrite existing annotation, or 0 to create new annotation. Omit to use default annotation

  • file: File to read from. Default to standard input if not specified

Options:

  • --name: A name for an annotation, only used when creating new annotations with 0, e.g. --name new_annotation

  • --replace-table: A table identifier with its replacement separated by a colon. You can also have multiple replacements by separating them with spaces, e.g. --replace-table 134779:134888 123444:135883

Label group settings are stored in JSON format and can be modified using an appropriate editor if desired.

omero pathviewer labelgroup updatetablelinks <object>

Command for initalizing tables linked to label image ROIs

Positional Arguments:

  • object: Image selector, e.g. Image:123