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
cellSens VSI	`cellsens.fail_on_missing_ets`	false	Throw an exception if an expected associated .ets file is missing
Gatan Digital Micrograph	`gatan.split_montage`	true	Split montage image tiles across multiple planes
Leica LAS AF LIF (Leica Image File Format)	`leicalif.old_physical_size`	false	Ensure physical pixel sizes are compatible with versions <= 5.3.2
Nikon NIS-Elements ND2	`nd2.chunkmap`	true	Use chunkmap table to read image offsets
Olympus ScanR	`scanr.skip_missing_wells`	true	Ignore missing wells
OME-TIFF	`ometiff.fail_on_missing_tiff`	true	Fail if a missing file is detected in a partial dataset
Ventana BIF	`ventana.split_tiles`	false	Report each tile as a separate series
Zeiss CZI	`zeissczi.attachments`	true	Include attachment images
Zeiss CZI	`zeissczi.autostitch`	true	Automatically stitch tiled images
Zeiss CZI	`zeissczi.trim_dimensions`	false	Trim XY dimensions to match those in ZEN
Zeiss CZI	`zeissczi.relative_positions`	false	Use pixel position instead of the physical stage position
CV7000	`cv7000.duplicate_missing_planes`	true	If set any missing planes will be replaced by the first plane in the channel. When set to false a blank plane will be returned.
Aperio SVS TIFF	`svs.remove_thumbnail`	true	If set the thumbnail image (if present) will not be available, and in particular will not be included in the pyramid. When set to false, the thumbnail image will be available for compatibility with versions <= 7.1.0.

Reader options can be used via the command line with showinf -option, in ImageJ via the configuration window, or via the API using the DynamicMetadataOptions class.

Format name	Option	Default	Description
OME-TIFF	`ometiff.companion`	None	If set, OME-XML will be written to a companion file with a name determined by the option value
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.
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.
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

Writer options can be used via the command line using bfconvert -option, or via the API using the DynamicMetadataOptions class.