Release of Bio-Formats 8.0.0 | Open Microscopy Environment (OME)

<!doctype html> <html class="no-js" lang="en" dir="ltr"> <head>  <script async src="https://www.googletagmanager.com/gtag/js?id=UA-49953125-6"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-49953125-6'); </script> <meta charset="utf-8" /> <meta http-equiv="x-ua-compatible" content="ie=edge" /> <meta name="viewport" content="width=device-width, initial-scale=1.0" /> <meta name="description" content="" /> <meta property="og:image" content="/img/logos/ome-logo_fb.png" /> <meta property="og:type" content="website" /> <meta property="og:url" content="" /> <meta property="og:title" content="The Open Microscopy Environment" /> <meta property="og:description" content="A consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data." /> <meta name="twitter:card" content="summary"> <meta name="twitter:title" content="The Open Microscopy Environment"> <meta name="twitter:image" content="https://www.openmicroscopy.org/img/logos/ome-logomark_twitter.png"> <title>Release of Bio-Formats 8.0.0 | Open Microscopy Environment (OME)</title>  <link rel="apple-touch-icon" sizes="180x180" href="/apple-touch-icon.png?v=2"> <link rel="icon" type="image/png" sizes="32x32" href="/favicon-32x32.png?v=2"> <link rel="icon" type="image/png" sizes="16x16" href="/favicon-16x16.png?v=2"> <link rel="manifest" href="/site.webmanifest?v=2"> <link rel="mask-icon" href="/safari-pinned-tab.svg?v=2" color="#5bbad5"> <link rel="shortcut icon" href="/favicon.ico?v=2"> <meta name="msapplication-TileColor" content="#2b5797"> <meta name="theme-color" content="#ffffff">  <link rel="me" href="https://fosstodon.org/@ome"/> <link rel="stylesheet" type="text/css" media="all" href="https://fonts.googleapis.com/css?family=Open+Sans:400,600,700,400italic,600italic,700italic"> <link rel="stylesheet" type="text/css" media="all" href="https://fonts.googleapis.com/css?family=Montserrat:400,500"> <link rel="stylesheet" type="text/css" media="all" href="/css/font-awesome.min.css"> <link rel="stylesheet" type="text/css" media="all" href="/css/foundation.min.css"> <link rel="stylesheet" type="text/css" media="all" href="/css/responsive-tables.css"> <link rel="stylesheet" type="text/css" media="all" href="/css/openmicroscopy.css"> </head> <body> <div class="title-bar" data-responsive-toggle="main-menu" data-hide-for="medium"> <button class="menu-icon" type="button" data-toggle></button> <div class="title-bar-title"></div> </div>  <div class="main-nav-bar top-bar" id="main-menu"> <div class="top-bar-left"> <ul class="vertical medium-horizontal dropdown menu" data-responsive-menu="accordion medium-dropdown"> <li class="hide-for-small-only"><a class="logo" href="/index.html"><img src="/img/logos/ome-main-nav.svg" alt="OME logo" /></a></li> <li class="show-for-small-only"><a href="/index.html"><img src="/img/logos/ome-logomark.svg" alt="OME logo" style="height:32px; width:32px;"/></a></li> <li class="has-submenu"><a href="/about/">About Us</a> <ul class="submenu menu vertical" data-submenu> <li><a href="/about/">Overview</a></li> <li><a href="/teams/">OME Teams</a></li> <li><a href="/contributors/">Contributors</a></li> <li><a href="/commercial-partners/">Commercial Partners</a></li> <li><a href="/licensing/">Licensing</a></li> <li><a href="/citing-ome/">Citing OME</a></li> <li><a href="/artwork/">Artwork</a></li> <li><a href="/training/">Training</a></li> <li><a href="/events/ome-community-meeting-2024/">OME 2024</a></li> </ul> </li> <li class="has-submenu"><a href="/news/">News</a> <ul class="submenu menu vertical" data-submenu> <li><a href="/news/">Overview</a></li> <li><a href="/announcements/">Announcements</a></li> <li><a href="/events/">Events</a></li> <li><a href="/minutes/">Minutes</a></li> <li><a href="/security/">Security</a></li> <li><a href="/careers/">Careers</a></li> <li><a href="/blog/">Blog</a></li> </ul> </li> </ul> </div> <div class="top-bar-right"> <ul class="vertical medium-horizontal dropdown menu" data-responsive-menu="accordion medium-dropdown"> <li class="has-submenu"><a href="/products/">Products</a> <ul class="submenu menu vertical" data-submenu> <li><a href="/products/">Overview</a></li> <li><a href="/omero/">OMERO</a></li> <li><a href="/bio-formats/">Bio-Formats</a></li> <li><a href="/ome-files/">OME Files</a></li> </ul> </li> <li class="has-submenu"><a href="/support/">Support</a> <ul class="submenu menu vertical" data-submenu> <li><a href="/support/">Overview</a></li> <li><a href="/security/">Security</a></li> <li><a href="/training/">Training</a></li> </ul> </li> <li><a href="/docs/">Docs</a></li> <li class="hide-for-small-only"><a href="/explore/" class="button btn-indigo" style="color: #eceff1; margin-left: 10px;">Explore</a></li> <li class="show-for-small-only"><a href="/explore/">Explore</a></li> </ul> </div> </div>  <a name="top-of-page"></a>  <div class="callout large primary" id="bg-image-announcements"> <div class="row column text-center"> <h1>Release of Bio-Formats 8.0.0</h1> <p>The OME team is pleased to announce the release of Bio-Formats 8.0.0</p> </div> </div> <hr class="invisible"> <div class="text-center"> <a id="back-to-top" href="/announcements/"><i class="fa fa-arrow-left"></i> back to Announcements</a> </div> <hr class="invisible"> <div class="row"> <div class="columns"> <p>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 <code class="language-plaintext highlighter-rouge">showinf</code> tool.</p> <p>The full list of changes included in this release are as follows:</p> <p>File format fixes and improvements:</p> <ul> <li>CV7000 <ul> <li>allow TIFF files to be in a subdirectory</li> </ul> </li> <li>DICOM <ul> <li>add support for reading precompressed tiles [1]</li> <li>improve image write performance [1]</li> <li>fix writing to DICOM when physical size units are missing from input data</li> </ul> </li> <li>Evident/Olympus OIR <ul> <li>improve image read performance (thanks to Nicolas Chiaruttini)</li> </ul> </li> <li>Hamamatsu NDPI <ul> <li>add support for reading precompressed tiles [1]</li> </ul> </li> <li>Leica LIF <ul> <li>fix file offset calculations for datasets with unstitched tiles</li> </ul> </li> <li>OME-TIFF <ul> <li>improve image write performance</li> <li>add support for writing precompressed tiles [1]</li> </ul> </li> <li>OME-XML <ul> <li>fix incorrect logical operators when checking image dimensions</li> </ul> </li> <li>RCPNL <ul> <li>define objective metadata for lens ID 18112</li> </ul> </li> <li>SDT <ul> <li>fix reading of files acquired with SPCM 9.90 (thanks to Chen Qian)</li> </ul> </li> <li>Zeiss LSM <ul> <li>fix incorrect logical operators when setting channel colors</li> </ul> </li> </ul> <p>Bio-Formats improvements:</p> <ul> <li>Add a batch processing feature to <code class="language-plaintext highlighter-rouge">showinf</code> (thanks to Torsten St枚ter)</li> <li>Update <code class="language-plaintext highlighter-rouge">bfconvert</code> to automatically detect the compression type when using <code class="language-plaintext highlighter-rouge">-precompressed</code> [1]</li> <li>Fix autoscaling of <code class="language-plaintext highlighter-rouge">float</code> values in <code class="language-plaintext highlighter-rouge">AWTImageTools</code></li> <li>ImageJ export plugin: fix handling of multi-channel datasets</li> <li><code class="language-plaintext highlighter-rouge">JPEGTurboService</code> [1] <ul> <li>add several new methods for retrieving tiles from a single JPEG stream</li> <li>expand Javadocs for existing methods</li> </ul> </li> </ul> <p>Documentation updates:</p> <ul> <li>update all links to AwareSystems TIFF documentation to last version from Internet Archive <ul> <li>see <a href="https://www.mail-archive.com/tiff@lists.osgeo.org/msg00421.html">libtiff mailing list discussion</a> for context</li> </ul> </li> <li>fix index of comannd-line tools</li> <li>add documentation for new batch processing feature in <code class="language-plaintext highlighter-rouge">showinf</code> (thanks to Torsten St枚ter)</li> <li>add documentation for precompressed tiles feature [1]</li> <li>several other fixes for broken links</li> </ul> <p>Component updates:</p> <ul> <li><code class="language-plaintext highlighter-rouge">ome-common</code> was upgraded to 6.0.24</li> <li><code class="language-plaintext highlighter-rouge">cdm-core</code> was upgraded to 5.6.0</li> </ul> <p>[1] This functionality was implemented through collaboration between Glencoe Software and <a href="https://datacommons.cancer.gov/repository/imaging-data-commons/">NCI Imaging Data Commons</a>, 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.</p> </div> </div> <div class="row"> <div class="column"> <p class="text-right"> — <i>October 24, 2024</i> </p> </div> </div>   <div class="text-center"> <a id="back-to-top" href="#top-of-page"><i class="fa fa-arrow-up"></i> back to top</a> </div>  <hr class="whitespace"> <div id="footer" class="callout large secondary"> <div class="row"> <div class="small-12 medium-4 columns"> <div class="medium-4"><a href="/index.html"><img class="footer-logo" src="/img/logos/ome-main-nav.svg" alt="OME logo" /></a></div> <p>© 2005-2024 University of Dundee & Open Microscopy Environment. <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">Creative Commons Attribution 4.0 International License</a></p> <p>OME source code is available under the <a href="https://www.gnu.org/copyleft/gpl.html">GNU General public license</a> or more permissive open source licenses, or through commercial license from <a href="https://www.glencoesoftware.com" target="_blank">Glencoe Software Inc.</a><br/>OME, Bio-Formats, OMERO, IDR and their associated logos are trademarks of <a href="https://www.glencoesoftware.com" target="_blank">Glencoe Software Inc.</a>, which holds these marks to protect them on behalf of the OME community.</p> <p class="tiny-print" style="float:left;">[ <a href="/site-map/">Site Map</a> ]</p> <p class="tiny-print" style="float:right;">Version: 2024.11.21</p> </div> <div class="medium-2 columns"> <h6>Learn About Us</h6> <ul class="menu vertical"> <li><a href="/about/">Who We Are</a></li> <li><a href="/teams/">Our Team</a></li> <li><a href="/explore/">What We Can Do</a></li> <li><a href="/news/">What We鈥檙e Up To</a></li> <li><a href="/events/ome-community-meeting-2024/">OME 2024</a></li> <li class="hide-for-large-only"> </li> </ul> </div> <div class="medium-2 columns"> <h6>Try Our Products</h6> <ul class="menu vertical"> <li><a href="/omero/downloads/">OMERO <span class="badge">Download</span></a></li> <li><a href="/bio-formats/downloads">Bio-Formats <span class="badge">Download</span></a></li> <li><a href="/ome-files/downloads">OME Files <span class="badge">Download</span></a></li> <li class="hide-for-large-only"> </li> </ul> </div> <div class="medium-2 columns"> <h6>Knowledge Base</h6> <ul class="menu vertical"> <li><a href="/support/">Support</a></li> <li><a href="/docs/">Documentation</a></li> <li><a href="https://omero-guides.readthedocs.io/">User Guides</a></li> <li><a href="https://www.openmicroscopy.org/forums">Forum</a></li> <li><a href="https://www.openmicroscopy.org/security/advisories/">Security Advisories</a></li> <li class="hide-for-large-only"> </li> </ul> </div> <div class="medium-2 columns end"> <h6>OME Public</h6> <ul class="menu vertical"> <li><a href="https://twitter.com/openmicroscopy" target="_blank"><i class="fa fa-fw fa-twitter"></i> Twitter</a></li> <li><a href="https://www.linkedin.com/company/ome---open-microscopy-environment" target="_blank"><i class="fa fa-fw fa-linkedin"></i> LinkedIn</a></li> <li><a href="https://www.facebook.com/openmicroscopy" target="_blank"><i class="fa fa-fw fa-facebook"></i> Facebook</a></li>  <li><a href="/on-the-web/" target="_blank"><i class="fa fa-globe"></i> On the Web</a></li> <li class="hide-for-large-only"> </li> </ul> </div> </div> </div> <script src="https://code.jquery.com/jquery-2.1.4.min.js"></script> <script src="/js/vendor/jquery.js"></script> <script src="/js/vendor/what-input.js"></script> <script src="/js/vendor/foundation.js"></script> <script src="/js/app.js"></script> <script src="/js/responsive-tables.js"></script> <script> $(document).foundation(); try { // helper function to filter out empty paths (trailing slash) var omitEmpty = function(el) { return el.trim() !== ''}; // extract last path bit from url var paths = document.location.pathname.split('/').filter(omitEmpty); var path = paths[paths.length-1]; // helper function to find and set active option var setActiveNavOption = function(el) { var subPaths = el.href.split('/').filter(omitEmpty); var subPath = subPaths[subPaths.length-1]; if (subPath === path) { $(el).addClass('is-active'); return true } return false; } // check if we have a .header-subnav match? var hasSubMenu = false; $(".header-subnav li a").each(function(i, el) { var isMatch = setActiveNavOption(el); if (isMatch) { hasSubMenu = true; return false; } }); // find corresponding path bit for .menu-subnav option if (hasSubMenu && paths.length > 1) { var parentPath = paths[paths.length-2]; if (parentPath !== 'omero') path = parentPath; } // set .menu-subnav option $(".menu-subnav li a").each(function(i, el) { if (setActiveNavOption(el)) return false; }); } catch(ignored) {} </script> </body> </html>

CINXE.COM

Release of Bio-Formats 8.0.0 | Open Microscopy Environment (OME)