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
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
Zeiss CZI	zeissczi.attachments	true	Include attachment images
Zeiss CZI	zeissczi.autostitch	true	Automatically stitch tiled images

Usage

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.

Writer options

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

Usage

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