diff --git a/_config.yml b/_config.yml index f7714054e..e8c752bf3 100644 --- a/_config.yml +++ b/_config.yml @@ -35,7 +35,7 @@ defaults: future: true bf: - version: 7.3.1 + version: 8.0.0 omero: version: 5.6.13 diff --git a/_data/bio-formats.json b/_data/bio-formats.json index 60c1396a6..a87854fbf 100644 --- a/_data/bio-formats.json +++ b/_data/bio-formats.json @@ -233,6 +233,9 @@ { "@id": "https://www.openmicroscopy.org/contributors#popiel" }, + { + "@id": "https://www.openmicroscopy.org/contributors#ChenQian" + }, { "@id": "https://www.openmicroscopy.org/contributors#VilleRantanen" }, diff --git a/_data/contributors.json b/_data/contributors.json index fe75f9ca2..69420e14c 100644 --- a/_data/contributors.json +++ b/_data/contributors.json @@ -165,6 +165,20 @@ "givenName": "Pierre", "sameAs": "https://github.com/ppouchin" }, + { + "@id": "https://www.openmicroscopy.org/contributors#ChenQian", + "@type": "Person", + "affiliation": [ + { + "@type": "Organization", + "name": "University of Gothenburg", + "url": "https://www.gu.se" + } + ], + "familyName": "Qian", + "givenName": "Chen", + "sameAs": "https://github.com/cqian89" + }, { "@id": "https://www.openmicroscopy.org/contributors#PaulVanSchayck", "@type": "Person", diff --git a/_posts/2024-10-24-bio-formats-8-0-0.md b/_posts/2024-10-24-bio-formats-8-0-0.md new file mode 100644 index 000000000..cba508205 --- /dev/null +++ b/_posts/2024-10-24-bio-formats-8-0-0.md @@ -0,0 +1,72 @@ +--- +layout: post +title: Release of Bio-Formats 8.0.0 +intro-blurb: The OME team is pleased to announce the release of Bio-Formats 8.0.0 +--- + +Today we are releasing Bio-Formats 8.0.0 which includes several performance improvements, expansion of the precompressed tile feature, and a new batch processing option in the `showinf` tool. + +The full list of changes included in this release are as follows: + +File format fixes and improvements: + +* CV7000 + - allow TIFF files to be in a subdirectory + +* DICOM + - add support for reading precompressed tiles [1] + - improve image write performance [1] + - fix writing to DICOM when physical size units are missing from input data + +* Evident/Olympus OIR + - improve image read performance (thanks to Nicolas Chiaruttini) + +* Hamamatsu NDPI + - add support for reading precompressed tiles [1] + +* Leica LIF + - fix file offset calculations for datasets with unstitched tiles + +* OME-TIFF + - improve image write performance + - add support for writing precompressed tiles [1] + +* OME-XML + - fix incorrect logical operators when checking image dimensions + +* RCPNL + - define objective metadata for lens ID 18112 + +* SDT + - fix reading of files acquired with SPCM 9.90 (thanks to Chen Qian) + +* Zeiss LSM + - fix incorrect logical operators when setting channel colors + +Bio-Formats improvements: + +* Add a batch processing feature to `showinf` (thanks to Torsten Stöter) +* Update `bfconvert` to automatically detect the compression type when using `-precompressed` [1] +* Fix autoscaling of `float` values in `AWTImageTools` +* ImageJ export plugin: fix handling of multi-channel datasets +* `JPEGTurboService` [1] + - add several new methods for retrieving tiles from a single JPEG stream + - expand Javadocs for existing methods + +Documentation updates: + +* update all links to AwareSystems TIFF documentation to last version from Internet Archive + - see [libtiff mailing list discussion](https://www.mail-archive.com/tiff@lists.osgeo.org/msg00421.html) for context +* fix index of comannd-line tools +* add documentation for new batch processing feature in `showinf` (thanks to Torsten Stöter) +* add documentation for precompressed tiles feature [1] +* several other fixes for broken links + +Component updates: + +* `ome-common` was upgraded to 6.0.24 +* `cdm-core` was upgraded to 5.6.0 + +[1] This functionality was implemented through collaboration between Glencoe Software and [NCI Imaging Data Commons](https://datacommons.cancer.gov/repository/imaging-data-commons/), +and has been funded in whole or in part with Federal funds from the National Cancer Institute, National Institutes +of Health, under Task Order No. HHSN26110071 under Contract No. HHSN2612015000031. diff --git a/bio-formats/downloads/index.html b/bio-formats/downloads/index.html index 2c142b032..cb65cd5a4 100644 --- a/bio-formats/downloads/index.html +++ b/bio-formats/downloads/index.html @@ -6,7 +6,7 @@

Bio-Formats {{ site.bf.version }} Downloads

- Read the Release Announcement + Read the Release Announcement Read the Docs
diff --git a/build.sh b/build.sh index fbdb8a3eb..498934044 100755 --- a/build.sh +++ b/build.sh @@ -8,7 +8,7 @@ docker pull jekyll/builder:pages docker run --rm -v $PWD:/srv/jekyll -eJEKYLL_UID=$UID jekyll/builder:pages jekyll build --config _config.yml,_prod.yml # Report 4xx status codes except 429 errors (Too Many Requests) # typically sent by GitHub while linkchecking the downloads -docker run --rm -v $(pwd)/_site:/site jekyll/builder:pages /usr/gem/bin/htmlproofer /site --only_4xx --ignore-status-codes "429" --ignore-files "/site/minutes/,/minutes/,/site/2014/,/site/2018/,/site/citing-ome/,/site/teams/,/site/about/" --ignore-urls "/www.icr.ac.uk/,/medium.com/pangeo/,/java.com/en/download/help/java_6.html/,/columbia.edu/,/eurobioimaging.eu/,/github.com/openmicroscopy/openmicroscopy/commit/,/icm-institute.org/wp-content/,/figure.openmicroscopy.org/demo/,/loci.wisc.edu/,/twitter.com/,/biovisioncenter.uzh.ch/,/www.dundee.ac.uk/locations/national-phenotypic-screening-centre-npsc/,/monash.edu/,/micronoxford.com/,/upf.edu/,/scientifica.uk.com/,/uk1s3.embassy.ebi.ac.uk/,/biorxiv.org/,/openmicroscopy.org/events/ome-community-meeting-2024/,/meded.hms.harvard.edu/,/loc.gov/,/royalsocietypublishing.org/,/science.1082602/,/www.softwarecollections.org/" --no-enforce-https --allow-missing-href --typhoeus='{"headers" : {"User-Agent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Brave Chrome/91.0.4472.164 Safari/537.36"}}' +docker run --rm -v $(pwd)/_site:/site jekyll/builder:pages /usr/gem/bin/htmlproofer /site --only_4xx --ignore-status-codes "429" --ignore-files "/site/minutes/,/minutes/,/site/2014/,/site/2018/,/site/citing-ome/,/site/teams/,/site/about/" --ignore-urls "/www.icr.ac.uk/,/medium.com/pangeo/,/java.com/en/download/help/java_6.html/,/columbia.edu/,/eurobioimaging.eu/,/github.com/openmicroscopy/openmicroscopy/commit/,/icm-institute.org/wp-content/,/figure.openmicroscopy.org/demo/,/loci.wisc.edu/,/twitter.com/,/biovisioncenter.uzh.ch/,/www.dundee.ac.uk/locations/national-phenotypic-screening-centre-npsc/,/monash.edu/,/micronoxford.com/,/upf.edu/,/scientifica.uk.com/,/uk1s3.embassy.ebi.ac.uk/,/biorxiv.org/,/openmicroscopy.org/events/ome-community-meeting-2024/,/meded.hms.harvard.edu/,/loc.gov/,/royalsocietypublishing.org/,/science.1082602/,/www.softwarecollections.org/,/www.facebook.com/openmicroscopy/,/sourceforge.net/p/icu/mailman/message/35232691/" --no-enforce-https --allow-missing-href --typhoeus='{"headers" : {"User-Agent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Brave Chrome/91.0.4472.164 Safari/537.36"}}' # Test file existence echo "Checking Schemas existence"