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	`nativend2.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

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

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