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

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.