# 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.
InCell 1000/2000 | `incell.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.

### 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
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

### Usage

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