Release of Bio-Formats 5.5.3



Dear all,

Bio-Formats 5.5.3 is now available for Fiji from the Java 8 update site which includes the following changes:

File format fixes and improvements:

Zeiss CZI
• fix to store Bézier ROIs as polygons, using the control points for the set of Bézier curves to form an approximation of the ROI
• improved parsing of stage positions in metadata
• improved parsing of detector gain values
• removed OME-XML validation errors by fixing potential for duplicate detector IDs
• removed invalid XML failures for Modulo label elements
• time increment metadata now populated on Pixels element
• fix to deal with consecutive empty planes in a series (thanks to Nicholas Trahearn)

• no longer allow core metadata to be modified when determining if files belong to a DICOM dataset

Nikon NIS-Elements ND2
• fixed calculation for scanline padding

Kodak BIP
• stricter file type checking enforced by no longer relying only on the file suffix

• improved parsing of metadata by correcting units for physical sizes, pixel type and capturing XYZ plane positions in OME-XML

Bio-Rad Gel
• fixed the width of pixel data offset field

• improved accuracy of format detection checking for input streams

Andor SIF
• fixed support for cropped images by parsing bounding box of the stored image

See for full details

The software is available at:

Any problems or comments, please use the OME Forums or mailing lists:


The OME Team