Additional reader and writer options

Some readers and writers have additional options which can be used to inform how Bio-Formats reads or writes files in that format.

Reader options

Format name	Option	Default	Description
:doc:`cellsens-vsi`	`cellsens.fail_on_missing_ets`	false	Throw an exception if an expected associated .ets file is missing
:doc:`gatan-digital-micrograph`	`gatan.split_montage`	true	Split montage image tiles across multiple planes
:doc:`leica-lif`	`leicalif.old_physical_size`	false	Ensure physical pixel sizes are compatible with versions <= 5.3.2
:doc:`nikon-nis-elements-nd2`	`nd2.chunkmap`	true	Use chunkmap table to read image offsets
:doc:`olympus-scanr`	`scanr.skip_missing_wells`	true	Ignore missing wells
:doc:`ome-tiff`	`ometiff.fail_on_missing_tiff`	true	Fail if a missing file is detected in a partial dataset
:doc:`ventana-bif`	`ventana.split_tiles`	false	Report each tile as a separate series
:doc:`zeiss-czi`	`zeissczi.attachments`	true	Include attachment images
:doc:`zeiss-czi`	`zeissczi.autostitch`	true	Automatically stitch tiled images
:doc:`zeiss-czi`	`zeissczi.trim_dimensions`	false	Trim XY dimensions to match those in ZEN
:doc:`zeiss-czi`	`zeissczi.relative_positions`	false	Use pixel position instead of the physical stage position

Format name	Option	Default	Description
:doc:`ome-tiff`	`ometiff.companion`	None	If set, OME-XML will be written to a companion file with a name determined by the option value
:doc:`ome-tiff`	`ometiff.preserve_creator`	false	If set to false, the OME-XML Creator attribute will be updated to include the current Bio-Formats version. This will overwrite any existing Creator in the input metadata. If set to true, the Creator attribute will only be updated if it wasn't previously set; any existing value will be preserved.
:doc:`ome-xml`	`omexml.preserve_creator`	false	If set to false, the OME-XML Creator attribute will be updated to include the current Bio-Formats version. This will overwrite any existing Creator in the input metadata. If set to true, the Creator attribute will only be updated if it wasn't previously set; any existing value will be preserved.
:doc:`dicom`	`dicom.dual_personality`	true	If set to true, DICOM files will be written as dual-personality DICOM/TIFF files which include TIFF metadata as described in Clunie DA. Dual-Personality DICOM-TIFF for Whole Slide Images: A Migration Technique for Legacy Software. J Pathol Inform. 2019 Apr 3;10:12. doi: 10.4103/jpi.jpi_93_18. PMID: 31057981; PMCID: PMC6489422.. If set to false, the writing of DICOM files will revert back to the original plain DICOM files