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 |
---|---|---|---|
|
false |
Throw an exception if an expected associated .ets file is missing |
|
|
true |
Split montage image tiles across multiple planes |
|
|
false |
Ensure physical pixel sizes are compatible with versions <= 5.3.2 |
|
|
true |
Use chunkmap table to read image offsets |
|
|
true |
Ignore missing wells |
|
|
true |
Fail if a missing file is detected in a partial dataset |
|
|
false |
Report each tile as a separate series |
|
|
true |
Include attachment images |
|
|
true |
Automatically stitch tiled images |
|
|
false |
Trim XY dimensions to match those in ZEN |
|
|
false |
Use pixel position instead of the physical stage position |
|
|
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 |
---|---|---|---|
|
None |
If set, OME-XML will be written to a companion file with a name determined by the option value |
|
|
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. |
|
|
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. |
|
|
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.