Release of OMERO and Bio-Formats 4.4.7

[Melissa Linkert-2]

The OME project is pleased to announce the release of OMERO and Bio-Formats 4.4.7.

Today we are launching 4.4.7, including several new features and bug fixes across all components.

For OMERO, this includes:

* usability and performance improvements in viewing of 'Big' tiled images;
* new permission features - import data and assign to another user ('Import As'), view all data from all users in a group at once;
* OMERO.web support for 'Split View Figure' and 'Thumbnail Figure' creation;
* OMERO.web support for copy-and-paste of rendering settings;
*  addition of several utility functions in the OMERO.matlab toolbox to load and manipulate objects from the server;
* review and testing of the C++ bindings;
* improved checksum calculation to detect errors on file upload;
* and the addition of array columns in OMERO.tables.

Bio-Formats improvements include fixes for the following formats:

* Amira - read files over 4 GiB;
* APNG -  remove dependency upon Java ImageIO;
* Bio-Rad Gel - improve pixel offset calculation;
* CellSens - prevent tag parsing errors;
* Deltavision - allow reading of truncated files, fix errors when importing into OMERO;
* FITS -  support truncated files;
* FV1000 - cope with missing thumbnails;
* Gatan - improve metadata parsing;
* Imaris HDF - correct channel count;
* Leica LIF - supported tiled images and parse User-Comment tags;
* Metamorph - correct channel count;
* Micromanager - correct file finding for single-channel datasets;
* Nikon ND2 - many improvements to metadata parsing
* SimplePCI - improve Z and T dimension calculation;
* Olympus SIS TIFF - read pixel sizes and exposure;
* Olympus ScanR - correct well linkage;
* TIFF - various fixes for reading tiled images
* Trestle - improve support for sub-resolutions;
* Zeiss CZI - parse Z positions, parse linescans, fix ordering of stitched files;
* Zeiss LSM and Zeiss ZVI - improve ROI parsing;
* improve export to multi-file datasets;
* and Bio-Formats now uses slf4j for logging rather than using log4j directly, enabling other logging implementations to be used, for example when Bio-Formats is used as a component in other software using a different logging system.

Full details are available on the OMERO Github milestone and the Bio-Formats Github milestone pages:
https://github.com/openmicroscopy/openmicroscopy/issues?milestone=5
https://github.com/openmicroscopy/bioformats/issues?milestone=4

As always, the software is available from http://www.openmicroscopy.org/site/products/omero/downloads and  http://www.openmicroscopy.org/site/products/bio-formats/downloads.


For information on the upgrade from OMERO 4.3 to 4.4, see the upgrade guide for system administrators (http://www.openmicroscopy.org/site/support/omero4/sysadmins/server-upgrade.html).

If you have not upgraded from 4.3 to 4.4 yet, then please upgrade directly to 4.4.7 as explained on the upgrade page linked above.

For full details of the next major release, see the https://trac.openmicroscopy.org.uk/ome/milestone/OMERO-4.4.8  milestone page.

Kind regards,
The OME team

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[Sebastian Rhode-4]

Hi,

when will the 4.4.7 release available via the Fiji Updater? My version
still say 4.4.5 and Fiji is up-to-date?

Cheers,

Sebi

Am Donnerstag, 25. April 2013 15:54:02 UTC+2 schrieb Melissa Linkert:

>
> The OME project is pleased to announce the release of OMERO and
> Bio-Formats 4.4.7.
>
> Today we are launching 4.4.7, including several new features and bug fixes
> across all components.
>
> For OMERO, this includes:
>
> * usability and performance improvements in viewing of 'Big' tiled images;
> * new permission features - import data and assign to another user
> ('Import As'), view all data from all users in a group at once;
> * OMERO.web support for 'Split View Figure' and 'Thumbnail Figure'
> creation;
> * OMERO.web support for copy-and-paste of rendering settings;
> *  addition of several utility functions in the OMERO.matlab toolbox to
> load and manipulate objects from the server;
> * review and testing of the C++ bindings;
> * improved checksum calculation to detect errors on file upload;
> * and the addition of array columns in OMERO.tables.
>
> Bio-Formats improvements include fixes for the following formats:
>
> * Amira - read files over 4 GiB;
> * APNG -  remove dependency upon Java ImageIO;
> * Bio-Rad Gel - improve pixel offset calculation;
> * CellSens - prevent tag parsing errors;
> * Deltavision - allow reading of truncated files, fix errors when
> importing into OMERO;
> * FITS -  support truncated files;
> * FV1000 - cope with missing thumbnails;
> * Gatan - improve metadata parsing;
> * Imaris HDF - correct channel count;
> * Leica LIF - supported tiled images and parse User-Comment tags;
> * Metamorph - correct channel count;
> * Micromanager - correct file finding for single-channel datasets;
> * Nikon ND2 - many improvements to metadata parsing
> * SimplePCI - improve Z and T dimension calculation;
> * Olympus SIS TIFF - read pixel sizes and exposure;
> * Olympus ScanR - correct well linkage;
> * TIFF - various fixes for reading tiled images
> * Trestle - improve support for sub-resolutions;
> * Zeiss CZI - parse Z positions, parse linescans, fix ordering of stitched
> files;
> * Zeiss LSM and Zeiss ZVI - improve ROI parsing;
> * improve export to multi-file datasets;
> * and Bio-Formats now uses slf4j for logging rather than using log4j
> directly, enabling other logging implementations to be used, for example
> when Bio-Formats is used as a component in other software using a different
> logging system.
>
> Full details are available on the OMERO Github milestone and the
> Bio-Formats Github milestone pages:
> https://github.com/openmicroscopy/openmicroscopy/issues?milestone=5 
> https://github.com/openmicroscopy/bioformats/issues?milestone=4 
>
> As always, the software is available from
> http://www.openmicroscopy.org/site/products/omero/downloads and  
> http://www.openmicroscopy.org/site/products/bio-formats/downloads.
>
>
> For information on the upgrade from OMERO 4.3 to 4.4, see the upgrade
> guide for system administrators (
> http://www.openmicroscopy.org/site/support/omero4/sysadmins/server-upgrade.html).
>
>
> If you have not upgraded from 4.3 to 4.4 yet, then please upgrade directly
> to 4.4.7 as explained on the upgrade page linked above.
>
> For full details of the next major release, see the
> https://trac.openmicroscopy.org.uk/ome/milestone/OMERO-4.4.8  milestone
> page.
>
> Kind regards,
> The OME team
>

... [show rest of quote]

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[ctrueden]

Hi Sebastian,

> when will the 4.4.7 release available via the Fiji Updater? My version
> still say 4.4.5 and Fiji is up-to-date?

If your Fiji is up to date, your version (seen via Help > About Plugins >
LOCI Plugins) should say "4.5-DEV".

Currently, Fiji provides builds from the 4.5.x "development" line (develop
branch of the Git repository), rather than from the 4.4.x "stable" line
(dev_4_4 branch).

For details, see:
    http://fiji.sc/Bio-Formats#Source_code

All bugfixes in the 4.4.x stable line should also be part of the 4.5.x
development line. If there is a recent bugfix you need that has not yet
been pushed to Fiji, let us know and I can upload a new version of 4.5.x.

Regards,
Curtis


On Tue, Apr 30, 2013 at 1:51 AM, Sebastian Rhode <[hidden email]> wrote:

> Hi,
>
> when will the 4.4.7 release available via the Fiji Updater? My version
> still say 4.4.5 and Fiji is up-to-date?
>
> Cheers,
>
> Sebi
>
> Am Donnerstag, 25. April 2013 15:54:02 UTC+2 schrieb Melissa Linkert:
>
>> The OME project is pleased to announce the release of OMERO and
>> Bio-Formats 4.4.7.
>>
>> Today we are launching 4.4.7, including several new features and bug
>> fixes across all components.
>>
>> For OMERO, this includes:
>>
>> * usability and performance improvements in viewing of 'Big' tiled
>> images;
>> * new permission features - import data and assign to another user
>> ('Import As'), view all data from all users in a group at once;
>> * OMERO.web support for 'Split View Figure' and 'Thumbnail Figure'
>> creation;
>> * OMERO.web support for copy-and-paste of rendering settings;
>> *  addition of several utility functions in the OMERO.matlab toolbox to
>> load and manipulate objects from the server;
>> * review and testing of the C++ bindings;
>> * improved checksum calculation to detect errors on file upload;
>> * and the addition of array columns in OMERO.tables.
>>
>> Bio-Formats improvements include fixes for the following formats:
>>
>> * Amira - read files over 4 GiB;
>> * APNG -  remove dependency upon Java ImageIO;
>> * Bio-Rad Gel - improve pixel offset calculation;
>> * CellSens - prevent tag parsing errors;
>> * Deltavision - allow reading of truncated files, fix errors when
>> importing into OMERO;
>> * FITS -  support truncated files;
>> * FV1000 - cope with missing thumbnails;
>> * Gatan - improve metadata parsing;
>> * Imaris HDF - correct channel count;
>> * Leica LIF - supported tiled images and parse User-Comment tags;
>> * Metamorph - correct channel count;
>> * Micromanager - correct file finding for single-channel datasets;
>> * Nikon ND2 - many improvements to metadata parsing
>> * SimplePCI - improve Z and T dimension calculation;
>> * Olympus SIS TIFF - read pixel sizes and exposure;
>> * Olympus ScanR - correct well linkage;
>> * TIFF - various fixes for reading tiled images
>> * Trestle - improve support for sub-resolutions;
>> * Zeiss CZI - parse Z positions, parse linescans, fix ordering of
>> stitched files;
>> * Zeiss LSM and Zeiss ZVI - improve ROI parsing;
>> * improve export to multi-file datasets;
>> * and Bio-Formats now uses slf4j for logging rather than using log4j
>> directly, enabling other logging implementations to be used, for example
>> when Bio-Formats is used as a component in other software using a different
>> logging system.
>>
>> Full details are available on the OMERO Github milestone and the
>> Bio-Formats Github milestone pages:
>> https://github.com/**openmicroscopy/openmicroscopy/**issues?milestone=5<https://github.com/openmicroscopy/openmicroscopy/issues?milestone=5>
>> https://github.com/**openmicroscopy/bioformats/**issues?milestone=4<https://github.com/openmicroscopy/bioformats/issues?milestone=4>
>>
>> As always, the software is available from http://www.openmicroscopy.org/*
>> *site/products/omero/downloads<http://www.openmicroscopy.org/site/products/omero/downloads>and
>> http://www.openmicroscopy.**org/site/products/bio-formats/**downloads<http://www.openmicroscopy.org/site/products/bio-formats/downloads>.
>>
>>
>>
>> For information on the upgrade from OMERO 4.3 to 4.4, see the upgrade
>> guide for system administrators (http://www.openmicroscopy.**
>> org/site/support/omero4/**sysadmins/server-upgrade.html<http://www.openmicroscopy.org/site/support/omero4/sysadmins/server-upgrade.html>
>> )**.
>>
>> If you have not upgraded from 4.3 to 4.4 yet, then please upgrade
>> directly to 4.4.7 as explained on the upgrade page linked above.
>>
>> For full details of the next major release, see the
>> https://trac.openmicroscopy.**org.uk/ome/milestone/OMERO-4.**4.8<https://trac.openmicroscopy.org.uk/ome/milestone/OMERO-4.4.8> milestone page.
>>
>> Kind regards,
>> The OME team
>>
>  --
> --
> Please avoid top-posting, and please make sure to reply-to-all!
>
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... [show rest of quote]

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[Sebastian Rhode-4]

Hi Curtis,

thanks for the quick answer.

Sebi

Am Donnerstag, 25. April 2013 15:54:02 UTC+2 schrieb Melissa Linkert:

>
> The OME project is pleased to announce the release of OMERO and
> Bio-Formats 4.4.7.
>
> Today we are launching 4.4.7, including several new features and bug fixes
> across all components.
>
> For OMERO, this includes:
>
> * usability and performance improvements in viewing of 'Big' tiled images;
> * new permission features - import data and assign to another user
> ('Import As'), view all data from all users in a group at once;
> * OMERO.web support for 'Split View Figure' and 'Thumbnail Figure'
> creation;
> * OMERO.web support for copy-and-paste of rendering settings;
> *  addition of several utility functions in the OMERO.matlab toolbox to
> load and manipulate objects from the server;
> * review and testing of the C++ bindings;
> * improved checksum calculation to detect errors on file upload;
> * and the addition of array columns in OMERO.tables.
>
> Bio-Formats improvements include fixes for the following formats:
>
> * Amira - read files over 4 GiB;
> * APNG -  remove dependency upon Java ImageIO;
> * Bio-Rad Gel - improve pixel offset calculation;
> * CellSens - prevent tag parsing errors;
> * Deltavision - allow reading of truncated files, fix errors when
> importing into OMERO;
> * FITS -  support truncated files;
> * FV1000 - cope with missing thumbnails;
> * Gatan - improve metadata parsing;
> * Imaris HDF - correct channel count;
> * Leica LIF - supported tiled images and parse User-Comment tags;
> * Metamorph - correct channel count;
> * Micromanager - correct file finding for single-channel datasets;
> * Nikon ND2 - many improvements to metadata parsing
> * SimplePCI - improve Z and T dimension calculation;
> * Olympus SIS TIFF - read pixel sizes and exposure;
> * Olympus ScanR - correct well linkage;
> * TIFF - various fixes for reading tiled images
> * Trestle - improve support for sub-resolutions;
> * Zeiss CZI - parse Z positions, parse linescans, fix ordering of stitched
> files;
> * Zeiss LSM and Zeiss ZVI - improve ROI parsing;
> * improve export to multi-file datasets;
> * and Bio-Formats now uses slf4j for logging rather than using log4j
> directly, enabling other logging implementations to be used, for example
> when Bio-Formats is used as a component in other software using a different
> logging system.
>
> Full details are available on the OMERO Github milestone and the
> Bio-Formats Github milestone pages:
> https://github.com/openmicroscopy/openmicroscopy/issues?milestone=5 
> https://github.com/openmicroscopy/bioformats/issues?milestone=4 
>
> As always, the software is available from
> http://www.openmicroscopy.org/site/products/omero/downloads and  
> http://www.openmicroscopy.org/site/products/bio-formats/downloads.
>
>
> For information on the upgrade from OMERO 4.3 to 4.4, see the upgrade
> guide for system administrators (
> http://www.openmicroscopy.org/site/support/omero4/sysadmins/server-upgrade.html).
>
>
> If you have not upgraded from 4.3 to 4.4 yet, then please upgrade directly
> to 4.4.7 as explained on the upgrade page linked above.
>
> For full details of the next major release, see the
> https://trac.openmicroscopy.org.uk/ome/milestone/OMERO-4.4.8  milestone
> page.
>
> Kind regards,
> The OME team
>

... [show rest of quote]

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