Merge pull request #663 from dgault/bf7.0.0

Bio-Formats 7.0.0 updates

_config.yml

@@ -35,7 +35,7 @@ defaults:
 future: true
 
 bf:
- version: 6.14.0
+ version: 7.0.0
 
 omero:
  version: 5.6.7

_data/bio-formats.json

@@ -68,6 +68,9 @@
         {
             "@id": "https://www.openmicroscopy.org/contributors#BarryDeZonia"
         },
+        {
+            "@id": "https://www.openmicroscopy.org/contributors#cgdogan"
+        },
         {
             "@id": "https://www.openmicroscopy.org/contributors#carandraug"
         },

_data/contributors.json

@@ -1538,6 +1538,13 @@
             "familyName": "Dornier",
             "givenName": "Rémy",
             "sameAs": "https://github.com/Rdornier"
+        },
+        {
+            "@id": "https://www.openmicroscopy.org/contributors#cgdogan",
+            "@type": "Person",
+            "familyName": "Dogan",
+            "givenName": "Can Gokhan",
+            "sameAs": "https://github.com/CGDogan"
         }
     ]
 }

_posts/2023-08-01-bio-formats-7-0-0.md

@@ -0,0 +1,67 @@
+---
+layout: post
+title: Release of Bio-Formats 7.0.0
+intro-blurb: The OME team is pleased to announce the release of Bio-Formats 7.0.0
+---
+
+Today we are releasing Bio-Formats 7.0.0 which includes support for writing dual-personality DICOM files. We 
+have also removed a number of previously deprecated components which rely on external libraries, most of which are 
+not well-supported. The full details of these are listed as below. For users who wish to retain support for files 
+using these readers or codecs, we recommend converting these file-sets to an actively maintained open format such as 
+OME-TIFF. This can be achieved using the Bio-Formats bfconvert command line tool as outlined in the 
+[command line tools documentation](https://bio-formats.readthedocs.io/en/stable/users/comlinetools/conversion.html).
+
+The full list of changes included in this release are as follows:
+
+Removal of deprecated components:
+* Legacy ND2 Reader
+   - The LegacyND2Reader and underlying components have been removed. This reader depended on 
+     an outdated DLL which had not been built in years, was untested and fully superseded by the 
+     new NativeND2Reader. The existing NativeND2Reader has been renamed as ND2Reader and now acts 
+     as the sole reader for the format. Support for the ND2 format will be unaffected and continue 
+     via this newly renamed reader.
+
+* Legacy QuickTime
+   - The LegacyQT Reader, Writer and Tools have been removed. These classes depended on the external 
+     QuickTime for Java library which is long obsolete. The existing NativeQTReader has been renamed 
+     as QTReader and support for QuickTime is now limited to non legacy readers and writers.
+
+* LuraWave Codec
+   - The LuraWave Codec along with the LuraWaveService and associated components have been removed and 
+     are no longer supported. This codec was dependent on a third-party proprietary library with a license 
+     code. This may impact LuraWave compressed files for the Opera Flex format.
+
+* Woolz
+   - The Woolz Reader, Writer and Service have been removed and are no longer supported. The reader and 
+     writer are untested and rely on an underlying library which has an unclear maintenance status.
+
+File format fixes and improvements:
+
+* DICOM
+   - Support has been added for the writing dual-personality DICOM/TIFF. The DICOM writer will now, by default, 
+     include TIFF metadata as described in 
+     [Clunie DA. Dual-Personality DICOM-TIFF for Whole Slide Images: A Migration Technique for Legacy Software. 
+       J Pathol Inform. 2019 Apr 3;10:12. doi: 10.4103/jpi.jpi_93_18. PMID: 31057981; PMCID: PMC6489422](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6489422). 
+     These new dual-personality files can be read either by the DICOM reader or can also be recognised as TIFF. A new 
+     option named `dicom.dual_personality` has been added to the DicomWriter. Setting this new option to false 
+     will revert writing of DICOM files back to the original plain DICOM files. This functionality was implemented 
+     through collaboration with [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.
+
+* PerkinElmer Opera Flex
+   - reader will now ignore files in which the compression cannot be identified
+
+* PerkinElmer Operetta
+   - fixed an exception when reading null planes (thanks to Nicolas Chiaruttini)
+
+Component updates:
+
+* `ome-common` was upgraded to 6.0.19
+* `ome-stubs` was upgraded to 6.0.1
+* `ome-codecs` was upgraded to 1.0.0
+* `native-lib-loader` was upgraded to 2.4.0 (thanks to Can Gokhan Dogan)
+
+Documentation improvements:
+
+* fixed a number of broken links

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 }}/2023/07/05/bio-formats-6-14-0.html" class="large btn-red button sites-button" style="text-shadow: none;">Read the Release Announcement</a>
+                <a href="{{ site.baseurl }}/2023/08/01/bio-formats-7-0-0.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>

events/ome-community-meeting-2020/speakers/index.html

@@ -75,7 +75,7 @@
     - firstname: Diane
       surname: Saunders
       aff: Vanderbilt University
-      link: "https://medicine.vumc.org/person/diane-saunders-phd"
+      link: "https://www.linkedin.com/in/dianecsaunders"
     - firstname: Nicholas
       surname: Soforniew
       aff: Chan Zuckerberg Initiative

index.html

@@ -68,7 +68,7 @@ <h1 class="show-for-small-only hero-main-header"><img src="{{ site.baseurl }}/im
               <br>
               <a href="{{ site.baseurl }}/events/" class="large button sites-button btn-red">Upcoming Workshops</a>
               &nbsp;&nbsp;
-              <a href="{{ site.baseurl }}/2023/07/25/omero-5-6-8.html" class="large button sites-button btn-red">Latest release</a>
+              <a href="{{ site.baseurl }}/2023/08/01/bio-formats-7-0-0.html" class="large button sites-button btn-red">Latest release</a>
               <br>
               <!--
               <a href="{{ site.baseurl }}/events/ome-community-meeting-2022/" class="large button sites-button btn-blue">OME 2022 Community Meeting</a>