Bio-Formats 7.0.1 updates

_config.yml

@@ -35,7 +35,7 @@ defaults:
 future: true
 
 bf:
- version: 7.0.0
+ version: 7.0.1
 
 omero:
  version: 5.6.9

_posts/2023-10-16-bio-formats-7-0-1.md

@@ -0,0 +1,73 @@
+---
+layout: post
+title: Release of Bio-Formats 7.0.1
+intro-blurb: The OME team is pleased to announce the release of Bio-Formats 7.0.1
+---
+
+Today we are releasing Bio-Formats 7.0.1 which includes a number of format improvements.
+
+The full list of changes included in this release are as follows:
+
+
+File format fixes and improvements:
+
+* Amersham Biosciences Gel
+   - improved format detection
+
+* Aperio SVS
+   - fixed a NullPointerException when attempting to read the magnification metadata
+   - physical sizes and positions are now calculated for full resolution label and macro images
+   - fixed a regression from Bio-Formats 6.8.0 which saw label and macro images incorrectly indexed
+
+* DICOM
+   - the DICOM writer will now throw an exception if the provided tiles don't match the 
+     expected tile size
+
+* Gatan DM3
+   - fixed a StringIndexOutOfBoundsException when parsing acquisition mode
+
+* Hamamatsu NDPI
+   - corrected for potential integer overflow in stored restart marker tag
+
+* IVision
+   - improved the version and data type checks in isThisType
+
+* Leica LIF
+   - improved the exception handling if no images are found
+
+* Olympus OIR
+   - fixed issue with XML block reading that resulted in missing pixel blocks
+
+* OME-TIFF
+   - reader will now fail fast and throw a FormatException if an invalid file is found
+
+* TIFF
+   - a FormatException is now thrown for unsupported 64-bit int data
+   - for all TIFF based formats the IFD entry offset is now checked before seeking
+
+* TillVision
+   - improved metadata parsing and detection of .pst files
+
+* Ventana
+   - fixed tile arithmetic for smallest resolutions
+
+* Zeiss CZI
+   - unified channel color parsing so that retrieving lookup tables now allows RGB and ARGB colors
+
+Bio-Formats improvements:
+
+* URLHandle will fall back to resetting stream if resetting to a mark fails
+* an exception will now be thrown if the TurboJPEG library fails to load (thanks to Can Gokhan Dogan)
+* fixed a Bio-Formats plugin bug when attempting to export a file after reducing the range of channels
+* reviewed and updated a number of file headers
+* updated GitHub Actions from checkout v2 to v3
+
+Component updates:
+
+* `ome-common` was upgraded to 6.0.20
+
+Documentation improvements:
+
+* fixed a number of broken external links
+* updated the link to OME Model documentation
+* migrated readthedocs configuration to version 2

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 }}/2023/08/01/bio-formats-7-0-0.html" class="large btn-red button sites-button" style="text-shadow: none;">Read the Release Announcement</a>
+                <a href="{{ site.baseurl }}/2023/10/16/bio-formats-7-0-1.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>

commercial-partners/index.html

@@ -102,7 +102,7 @@ <h5 class="text-center">Organizations supporting OME-TIFF</h5>
             <div class="column"><a target="_blank" href="http://www.perkinelmer.com/"><div class="card-consortium card"><div class="card-section">PerkinElmer Life and Analytical Sciences Inc.</div></div></a></div>
             <div class="column"><a target="_blank" href="http://www.scientifica.uk.com"><div class="card-consortium card"><div class="card-section">Scientifica</div></div></a></div>
             <div class="column"><a target="_blank" href="http://www.svi.nl/"><div class="card-consortium card"><div class="card-section">Scientific Volume Imaging B.V.</div></div></a></div>
-            <div class="column"><a target="_blank" href="http://www.till-photonics.com/"><div class="card-consortium card"><div class="card-section">TILL Photonics GmbH</div></div></a></div>
+            <div class="column"><a target="_blank" href="http://www.fei.com/"><div class="card-consortium card"><div class="card-section">TILL Photonics GmbH, now FEI Munich</div></div></a></div>
             <div class="column"><a target="_blank" href="https://www.visiopharm.com/"><div class="card-consortium card"><div class="card-section">Visiopharm</div></div></a></div>
             <hr class="whitespace">
             <div class="row small-up-2 medium-up-2">

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 }}/2023/10/02/omero-5-6-9.html" class="large button sites-button btn-red">Latest release</a>
+              <a href="{{ site.baseurl }}/2023/10/16/bio-formats-7-0-1.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>