Bio-Formats

Bio-Formats Downloads
Licensing

Page Contents

Previous topic

Grouping files using a pattern file

This Page

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
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.