bioformats Profile
bioformats

@bioformats

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535

OME Bio-Formats development status

Joined July 2008
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@bioformats
bioformats
1 year
A new Bio-Formats version 7.3.0 has been released. It includes compatibility for Bio-Formats with Java-21 alongside a number of format improvements including updates for DICOM, CellSens VSI, and PerkinElmer Columbus. For full details see the announcement,
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openmicroscopy.org
A consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data.
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@bioformats
bioformats
2 years
A new Bio-Formats version has been released, Version 7.0.1 is out. It includes fixes for many formats including updates for Aperio SVS and Zeiss CZI. Check the release announcement for more details,
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openmicroscopy.org
A consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data.
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@bioformats
bioformats
3 years
In case you missed it, Bio-Formats 6.10.1 was released yesterday including a few format fixes and a few dependency upgrades. See for more details.
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openmicroscopy.org
A consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data.
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@bioformats
bioformats
3 years
RT @openmicroscopy: Very proud to release of OMERO.server 5.6.5 including:. - new server configuration for large floating-point images (tha….
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openmicroscopy.org
A consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data.
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@bioformats
bioformats
3 years
Check out for the announcement of the latest Bio-Formats release. Includes an updated QPTIFF reader (partnership between @GlencoeSoftware @AkoyaBio), a new Slidebook7 reader (contributed by @3i_inc) and several other format fixes and dependency updates.
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openmicroscopy.org
A consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data.
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@bioformats
bioformats
3 years
Using the opportunity to promote the recent release of Bio-Formats 6.9.1. Includes bug fixes and performance improvements esp. from @GlencoeSoftware and @nKiaru and an upgrade of the netcdf-java library using by Bio-Formats - see for full details.
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openmicroscopy.org
A consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data.
@openmicroscopy
openmicroscopy
3 years
A new version of OMERO.server is finally out! Version 5.6.4 is out. It includes Bio-Formats 6.9.1. Check the release announcement for more details. See
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@bioformats
bioformats
4 years
Several new file formats added and updates in Bio-Formats 6.9.0. Thanks to @leicamicro (new Leica LOF/XLEF readers), @nKiaru (PE Operetta) @zacsimile (Leica LIF), Nils Gladitz (Imspector OBF). Great to see more industrial contribs to key #opensource community library.
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@bioformats
bioformats
4 years
In case you missed it, Bio-Formats 6.8.1 was released yesterday Includes a few bug fixes as well as the removal of the deprecated loci_tools bundle - see
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openmicroscopy.org
A consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data.
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@bioformats
bioformats
4 years
For users who are concerned, the workaround is simply to use the `bioformats_package.jar` bundle which provides the same functionalities using a different logging framework. `loci_tools.jar` will be removed in the next release of Bio-Formats.
@openmicroscopy
openmicroscopy
4 years
Worried about the impact of Log4Shell (CVE-2021-44228) on OMERO or Bio-Formats? The short answer is "none" and "only when using loci_tools.jar", respectively. Please see our recent post on the #imagesc forum for more information:.
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@bioformats
bioformats
4 years
@GlencoeSoftware @Olympus @zeiss_micro Last but not least, Bio-Formats now reads/writes #DICOM WSI format!. Amazing work done in collaboration between @GlencoeSoftware and #NCI Imaging Data Commons, funded from the National Cancer Institute, NIH and released under the permissive BSD-2 license.
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@bioformats
bioformats
4 years
Bio-Formats 6.8.0 also includes the result of two new successful partnerships with @GlencoeSoftware: support for the @Olympus omp2info format and support for zstd compression in the @zeiss_micro CZI format.
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@bioformats
bioformats
4 years
Last release of 2021: see for the announcement of Bio-Formats 6.8.0!. As always thanks to our community for their contributions.
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openmicroscopy.org
A consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data.
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@bioformats
bioformats
4 years
". [The analysis] details OME’s previous experiences trying to bridge this tension and, along with [the main text], underscores the need for a new chunked, parallelized data storage and access mechanism, enabling advanced AI applications and public data resources.".
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@bioformats
bioformats
4 years
A direct link: ."For 15 years, OME has provided the community an alternative to a common file format, namely the Bio-Formats translation library. .
@openmicroscopy
openmicroscopy
4 years
Be sure to check out the supplemental note covering the challenges of translating proprietary formats with @bioformats and our view of history and current status of formats and importance of #OMENGFF.
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@bioformats
bioformats
4 years
RT @openmicroscopy: Be sure to check out the supplemental note covering the challenges of translating proprietary formats with @bioformats….
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@bioformats
bioformats
4 years
RT @TalleyJLambert: The 4.2 release of aicsimageio brings support for Bio-Formats to the already-great python image reader!. .
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@bioformats
bioformats
4 years
Finally, we are also very glad to read that @LeicaMicro is working on a reader for the .log/.xlef file formats for inclusion in a future Bio-Formats release. Looking forward to this contribution.
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@bioformats
bioformats
4 years
This release also relicenses several components to the permissive BSD-2 license to maximize their re-usability including:. - the readers/writers for the open CellH5, BDV and KLB file formats.- the functions used by the Bio-Formats MATLAB toolbox/GNU Octave bindings.
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@bioformats
bioformats
4 years
Bio-Formats 6.7.0 is out today with several file formats fixes and dependency updates. Check out for the full details. As always, huge thanks for the direct contributions from the #bioimaging community.
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openmicroscopy.org
A consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data.
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