Merge pull request #757 from melissalinkert/bf-8.0.0

Updates for Bio-Formats 8.0.0

_config.yml

@@ -35,7 +35,7 @@ defaults:
 future: true
 
 bf:
- version: 7.3.1
+ version: 8.0.0
 
 omero:
  version: 5.6.13

_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"
         },

_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",

_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/[email protected]/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.

bio-formats/downloads/index.html

@@ -6,7 +6,7 @@
         <div class="callout large primary" id="bg-image-bio-formats">
             <div class="row column text-center">
                 <h1>Bio-Formats {{ site.bf.version }} Downloads</h1>
-                <a href="{{ site.baseurl }}/2024/07/11/bio-formats-7-3-1.html" class="large btn-red button sites-button" style="text-shadow: none;">Read the Release Announcement</a>
+                <a href="{{ site.baseurl }}/2024/10/24/bio-formats-8-0-0.html" class="large btn-red button sites-button" style="text-shadow: none;">Read the Release Announcement</a>
                 <a href="https://docs.openmicroscopy.org/bio-formats/{{ site.bf.version }}/" target="_blank" class="hero-link">Read the Docs</a>
             </div>
         </div>

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"