Release of Bio-Formats 5.1.9

[Jean-Marie Burel (Staff)]

Dear All,
Today we are releasing Bio-Formats 5.1.9, a point release focusing on bug
fixing:
Java bug fixes, including:

* SDT
* fixed width padding calculation for single-pixel image


* Deltavision
* fixed the parsing of the new date format
* added support for parsing and storing the working distance in native
units


* Micromanager
* cleaned up JSON metadata parsing


* Olympus Fluoview
* fixed null pointer exceptions while parsing metadata


* Leica LIF
* fixed large multi-tiled files from having incorrect plane offsets after
the 2GB mark


* EM formats (MRC and Spider)
* added native length support for EM readers


* Gatan
* fixed erroneous metadata parsing
* added support for parsing and storing the physical sizes in native units


* OME-TIFF
* improved handling of OME-TIFF multi-file fileset¹s with partial metadata
blocks


* Nikon ND2
* fixed the parsing of emission wavelength


* Olympus CellR (APL)
* fixed multiple parsing issues with the mtb file


* SlideBook6
* removed slidebook dlls from Bio-Formats repository*


* Zeiss CZI
* fixed parsing of files with multiple mosaics and positions



Documentation updates, including:

* improved documentation for the export of BigTIFFs in ImageJ

C++:

* no changes

*This is a breaking change for the Slidebook6Reader - users should visit
http://www.openmicroscopy.org/info/slidebook for further information as
the native binary files required for this reader are now hosted on an
update site which you will need to enable for the reader to work once you
have upgraded.
The software is available at:
http://downloads.openmicroscopy.org/bio-formats/5.1.9
Any problems or comments, please use the OME Forums or mailing lists:
http://www.openmicroscopy.org/site/community
Regards,
The OME Team


The University of Dundee is a registered Scottish Charity, No: SC015096

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[Lendl,Thomas]

Dear OME Team,

I did the update but unfortunately I still cannot open files (multiposition 3D timeseries) from ZEN2 in Fiji. I would be grateful if you could put this on your list to get it fixed.

Best regards,
Thomas

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Jean-Marie Burel (Staff)
Sent: Montag, 18. April 2016 18:14
To: [hidden email]
Subject: Release of Bio-Formats 5.1.9

Dear All,
Today we are releasing Bio-Formats 5.1.9, a point release focusing on bug
fixing:
Java bug fixes, including:

* SDT
* fixed width padding calculation for single-pixel image


* Deltavision
* fixed the parsing of the new date format
* added support for parsing and storing the working distance in native units


* Micromanager
* cleaned up JSON metadata parsing


* Olympus Fluoview
* fixed null pointer exceptions while parsing metadata


* Leica LIF
* fixed large multi-tiled files from having incorrect plane offsets after the 2GB mark


* EM formats (MRC and Spider)
* added native length support for EM readers


* Gatan
* fixed erroneous metadata parsing
* added support for parsing and storing the physical sizes in native units


* OME-TIFF
* improved handling of OME-TIFF multi-file fileset¹s with partial metadata blocks


* Nikon ND2
* fixed the parsing of emission wavelength


* Olympus CellR (APL)
* fixed multiple parsing issues with the mtb file


* SlideBook6
* removed slidebook dlls from Bio-Formats repository*


* Zeiss CZI
* fixed parsing of files with multiple mosaics and positions



Documentation updates, including:

* improved documentation for the export of BigTIFFs in ImageJ

C++:

* no changes

*This is a breaking change for the Slidebook6Reader - users should visit http://www.openmicroscopy.org/info/slidebook for further information as the native binary files required for this reader are now hosted on an update site which you will need to enable for the reader to work once you have upgraded.
The software is available at:
http://downloads.openmicroscopy.org/bio-formats/5.1.9
Any problems or comments, please use the OME Forums or mailing lists:
http://www.openmicroscopy.org/site/community
Regards,
The OME Team


The University of Dundee is a registered Scottish Charity, No: SC015096

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[Roger Leigh-2]

On 19/04/2016 11:37, Lendl,Thomas wrote:
> Dear OME Team,
>
> I did the update but unfortunately I still cannot open files (multiposition 3D timeseries) from ZEN2 in Fiji. I would be grateful if you could put this on your list to get it fixed.

Dear Thomas,

Please see https://trac.openmicroscopy.org/ome/ticket/12935 for our open
ticket for this issue.  If you would like adding to the Cc on this
ticket, please let me know and I'll add you.  You will then get notified
when this ticket is updated with any changes.


Kind regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
School of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: [phone]

The University of Dundee is a registered Scottish Charity, No: SC015096

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