<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
Hi Aaron,
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 14 Dec 2018, at 10:00, Ponti Aaron <<a href="mailto:aaron.ponti@bsse.ethz.ch" class="">aaron.ponti@bsse.ethz.ch</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Hello,<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
we have .FLI files from Lambert Instruments' Capture software (version 1.0.4.0) for the high-speed camera HiCAM FLUO. Images are streamed at high speed and stored as UINT12 (2 pixels in 3 bytes) or optionally as UINT8. The FLIM reader in bio-formats (<a href="https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/LiFlimReader.java" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/LiFlimReader.java</a>)
does not seem to support 12-bit intensities. </div>
</div>
</div>
</blockquote>
<div><br class="">
</div>
<div>From the internal specification of the LI-FLIM file format which we used for the reader [1]:</div>
<div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><br class="">
</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">"The datatype key can have one of the following 8 values: UINT8, INT8, UINT16, INT16,</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">UINT32, INT32, REAL32 or REAL64.”</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class=""><br class="">
</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">A file that would use UINT12 would probably be a new variant of the file format for which we</div>
<div style="margin: 0px; font-stretch: normal; line-height: normal;" class="">have currently neither a format specification nor representative samples</div>
<div class=""><br class="">
</div>
</div>
<blockquote type="cite" class="">
<div class="">
<div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
Also, when asking bio-formats to return the metadata, the whole file is returned (which suggests that the metadata of standard FLIM .FLI files is organized -- or terminated -- differently).</div>
</div>
</div>
</blockquote>
<div><br class="">
</div>
<div>Understood. This would be consistent with the pixel type issue reported above i.e. that could</div>
<div>indeed reflect an internal layout different from the one Bio-Formats is expecting..</div>
<div><br class="">
</div>
<blockquote type="cite" class="">
<div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p><span style="font-size: 11pt;" class="">The file is binary with the first bytes containing metadata information in readable text format. One field is 'hasDarkImage'. If hasDarkImage == 1, the very last frame is a dark image that is subtracted
on-the-fly in the software when displaying the frames (but the images are stored raw in the file). The 'exposureTime' is in micro seconds. Finally, the software seems to support 'compression', although there is no setting for turning it on in the software.
The software supports binning.</span></div>
</div>
</blockquote>
<br class="">
<blockquote type="cite" class="">
<div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p><span style="font-size: 11pt;" class="">Would you be interested in adding support for these files to bio-formats? We have example files that we could upload.</span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
</div>
</div>
</blockquote>
<div><br class="">
</div>
<div>Over the past years, we have been working on ways to have more sustainable support for new file</div>
<div>formats including any variants of existing file formats. We published a blog post summarizing our</div>
<div>experience a few years ago [2] and since then more manufacturers have been engaging in this</div>
<div>process.</div>
<div><br class="">
</div>
<div>Have you been in touch with Lambert Instruments to report this issue? Are they aware that the latest files</div>
<div>produced by their software are no longer readable by Bio-Formats and any software based upon it?</div>
<div><br class="">
</div>
<div>Representative samples allowing to reproduce the issue are always welcome. Ideally public samples licensed</div>
<div>under CC-BY license [3] are the most effective way to help spontaneous or sponsored contributions to the</div>
<div>project and facilitate both the immediate software work as well as the long-term maintenance.</div>
<div>You can upload datasets under 2GB to our QA system [4] and we can provide FTP credentials for large samples.</div>
<div><br class="">
</div>
<div>Best,</div>
<div>Sebastien</div>
<div><br class="">
</div>
<div><br class="">
</div>
<div>
<div>[1] <a href="https://docs.openmicroscopy.org/bio-formats/5.9.2/formats/lambert-instruments-flim.html" class="">https://docs.openmicroscopy.org/bio-formats/5.9.2/formats/lambert-instruments-flim.html</a></div>
<div>[2] <a href="https://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/" class="">https://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/</a></div>
<div>[3] <a href="https://downloads.openmicroscopy.org/images/" class="">https://downloads.openmicroscopy.org/images/</a></div>
<div>[4] <a href="http://qa.openmicroscopy.org.uk/qa/upload/" class="">http://qa.openmicroscopy.org.uk/qa/upload/</a></div>
<div class=""><br class="">
</div>
</div>
<div><br class="">
</div>
<blockquote type="cite" class="">
<div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p><span style="font-size: 11pt;" class="">Thanks a lot,</span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
a2<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
</div>
</blockquote>
<div><br class="">
</div>
</div>
<div>
<blockquote type="cite" class="">
<div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
----<o:p class=""></o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="color: rgb(31, 73, 125);" class="">Dr. Aaron Ponti<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="color: rgb(31, 73, 125);" class="">Software and Data Management Engineer<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="color: rgb(31, 73, 125);" class="">Image Analysis Specialist<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="color: rgb(31, 73, 125);" class="">Single Cell Facility<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span style="color: rgb(31, 73, 125);" class="">Department of Biosystems Science and Engineering (D-BSSE)<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">ETH Zürich<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">Office 2.30<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">Mattenstrasse 26<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">4058 Basel, Switzerland<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="DE-CH" style="color: rgb(31, 73, 125);" class=""><a href="mailto:aaron.ponti@bsse.ethz.ch" style="color: rgb(149, 79, 114); text-decoration: underline;" class=""><span style="color: rgb(5, 99, 193);" class="">aaron.ponti@bsse.ethz.ch</span></a><o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">T: +41 61 387 33 74<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">F: +41 61 387 39 93<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<o:p class=""> </o:p></div>
</div>
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">ome-users
mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">ome-users@lists.openmicroscopy.org.uk</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" style="color: rgb(149, 79, 114); text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a></blockquote>
</div>
<br class="">
</div>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</body>
</html>