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Hi Johan,
<div class=""><br class="">
</div>
<div class="">Many thanks for opening the PR, external contributions to the project are always appreciated.</div>
<div class="">We have included the PR for testing with our build systems and will review it shortly.</div>
<div class=""><br class="">
</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 22 Jan 2019, at 17:47, Johan Herz <<a href="mailto:johan@lambertinstruments.com" class="">johan@lambertinstruments.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="auto" class="">Hello Sebastien,
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">Regarding UINT12, I made a pull request for updating our LiFLIMreader.java (<a href="https://github.com/openmicroscopy/bioformats/pull/3308" class="">https://github.com/openmicroscopy/bioformats/pull/3308</a>)</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">Please let me know if this is okay, many thanks in advance.</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">Looking forward to receiving your reply.</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">Best,</div>
<div dir="auto" class="">Johan Herz</div>
<div dir="auto" class=""><br class="">
</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="">Op ma 21 jan. 2019 09:12 schreef Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" class="">s.besson@dundee.ac.uk</a>:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word;line-break:after-white-space" class="">Good morning Johan,
<div class=""><br class="">
</div>
<div class="">The OME handling of 12-bit data is very similar to what you do in your viewer. Shortly,</div>
<div class="">the model allows to define the pixel type [1] but also the significant number of bits [2] for</div>
<div class="">A dataset.</div>
<div class=""><br class="">
</div>
<div class="">There is no immediate plan to extend the pixel types but you can see examples of using</div>
<div class="">These concepts to read 12-bit data for other file readers [3] [4].</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class="">[1] <a href="https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#PixelType" target="_blank" rel="noreferrer" class="">https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#PixelType</a> </div>
<div class="">[2] <a href="https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Pixels_SignificantBits" target="_blank" rel="noreferrer" class="">https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Pixels_SignificantBits</a> </div>
<div class="">[3] <a href="https://github.com/openmicroscopy/bioformats/blob/v5.9.2/components/formats-gpl/src/loci/formats/in/CanonRawReader.java#L133" target="_blank" rel="noreferrer" class="">https://github.com/openmicroscopy/bioformats/blob/v5.9.2/components/formats-gpl/src/loci/formats/in/CanonRawReader.java#L133</a> </div>
<div class="">[4] <a href="https://github.com/openmicroscopy/bioformats/blob/v5.9.2/components/formats-gpl/src/loci/formats/in/ScanrReader.java#L591" target="_blank" rel="noreferrer" class="">https://github.com/openmicroscopy/bioformats/blob/v5.9.2/components/formats-gpl/src/loci/formats/in/ScanrReader.java#L591</a> <br class="">
<div class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On 18 Jan 2019, at 14:16, Johan Herz <<a href="mailto:johan@lambertinstruments.com" target="_blank" rel="noreferrer" class="">johan@lambertinstruments.com</a>> wrote:</div>
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<div class="">
<div dir="ltr" class="">Hello Sebastien,
<div class=""><br class="">
</div>
<div class="">Thank you and your welcome.</div>
<div class="">one of the reasons we use uint12 is that it preserves disk space. If we finally present the data in our viewer we upscale it to 16bit. </div>
<div class="">When do you think uint12 will become available in the core metadata? Would it be an option to add an 'unpacker'-function to the LiFLIMReader, that unpacks and upscales the uint12 to uint16 data? But can the data still be opened virtually in that
case?</div>
<div class=""><br clear="all" class="">
<div class="">
<div dir="ltr" class="m_-5160481645704919580m_-4377294682811180876gmail_signature" data-smartmail="gmail_signature">
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<div class="">
<div dir="ltr" class="">
<div dir="ltr" class=""><span style="font-size:12.8px" class="">Best regards,</span><br class="">
</div>
<div dir="ltr" class=""><br style="font-size:12.8px" class="">
<span style="font-size:12.8px" class="">Johan Herz, Sales Engineer </span><br style="font-size:12.8px" class="">
<span style="font-size:12.8px" class=""><br class="">
</span></div>
<div dir="ltr" class="">Please visit <a href="http://flim.camera/" target="_blank" rel="noreferrer" class="">FLIM.camera</a> for more information about the Toggel.</div>
<div dir="ltr" class=""><span style="font-size:12.8px" class=""><br class="">
</span></div>
<div dir="ltr" class="">
<div dir="ltr" style="font-size:12.8px" class=""><span style="font-size:12.8px" class="">Tel: +31-50-501-8461 | Skype: lambert-</span>johan<br class="">
</div>
<div dir="ltr" style="font-size:12.8px" class=""><span style="font-size:12.8px" class="">Lambert Instruments BV|Leonard Springerlaan 19 (5th floor)|9727 KB Groningen|The Netherlands</span><br style="font-size:12.8px" class="">
<span style="font-size:12.8px" class="">Dutch Chamber of Commerce nr.: 52396940 | </span><a href="http://www.lambertinstruments.com/" style="font-size:12.8px" target="_blank" rel="noreferrer" class="">www.lambertinstruments.com</a></div>
</div>
</div>
</div>
</div>
</div>
</div>
<br class="">
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="m_-5160481645704919580m_-4377294682811180876gmail_attr">Op di 15 jan. 2019 om 12:29 schreef Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" target="_blank" rel="noreferrer" class="">s.besson@dundee.ac.uk</a>>:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="">Hi Johan,
<div class=""><br class="">
</div>
<div class="">Thank you very much for opening the Pull Request and sending us representative</div>
<div class="">samples of the issue. We will review it at earliest and hopefully have at least this fix</div>
<div class="">released as part of Bio-Formats 6.</div>
<div class=""><br class="">
</div>
<div class="">One comment regarding the data format.The pixel type is part of what we call core</div>
<div class="">metadata i.e. metadata mandatory for describing each image in a fileset. It can only</div>
<div class="">take a limited number of values [1]. This is partly why the mapping of this particular</div>
<div class="">metadata field is much stricter than other types of keys [2] and will need to be updated</div>
<div class="">In order to extend support for new data types.</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class="">[1] <font color="#0069d9" class=""><span class=""><u class=""><a href="https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#PixelType" target="_blank" rel="noreferrer" class="">https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#PixelType</a></u></span></font></div>
<div class="">[2] <a href="https://github.com/openmicroscopy/bioformats/blob/v5.9.2/components/formats-gpl/src/loci/formats/in/LiFlimReader.java#L496" target="_blank" rel="noreferrer" class="">https://github.com/openmicroscopy/bioformats/blob/v5.9.2/components/formats-gpl/src/loci/formats/in/LiFlimReader.java#L496</a></div>
<div class=""><font color="#0069d9" class=""><span class=""><u class=""><br class="">
</u></span></font></div>
<div class="">
<blockquote type="cite" class="">
<div class="">On 14 Jan 2019, at 19:17, Johan Herz <<a href="mailto:johan@lambertinstruments.com" target="_blank" rel="noreferrer" class="">johan@lambertinstruments.com</a>> wrote:</div>
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<div class="">
<div dir="auto" class="">
<div class="">Hello Sebastien,</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">The GB file size problem persisted, and we think the following pull request will fix it: <a href="https://github.com/openmicroscopy/bioformats/pull/3303" target="_blank" rel="noreferrer" class="">https://github.com/openmicroscopy/bioformats/pull/3303</a></div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">If you have any reconmondations please let me know.</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">Regarding implementing the unsigned 12 bit data format, please let me know if I can be of any further help.</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">Many thabks for your support.</div>
<div dir="auto" class=""><br class="">
</div>
<div dir="auto" class="">Best,</div>
<div dir="auto" class="">Johan</div>
<div dir="auto" class=""><br class="">
<div class="gmail_quote" dir="auto">
<div dir="ltr" class="">Op ma 14 jan. 2019 10:57 schreef Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" target="_blank" rel="noreferrer" class="">s.besson@dundee.ac.uk</a>:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="">Hi Johan and Aaron,
<div class=""><br class="">
</div>
<div class="">Happy New Year to you guys too. I am reincluding the Users mailing lists in this</div>
<div class="">conversation.</div>
<div class="">
<div class=""><br class="">
</div>
<div class="">
<blockquote type="cite" class="">
<div class="">On 11 Jan 2019, at 08:11, Johan Herz <<a href="mailto:johan@lambertinstruments.com" rel="noreferrer noreferrer" target="_blank" class="">johan@lambertinstruments.com</a>> wrote:</div>
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<div class="">
<div dir="ltr" class="">
<div dir="ltr" class="">Hello Sebastien and Ponti,</div>
<div dir="ltr" class=""><br class="">
</div>
<div class="">Thank you for the follow-up, all to you too a very good 2019!</div>
<div class=""><br class="">
</div>
<div class="">@Aaron, yes I will be available for testing, my pleasure.<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">@Sebastien, The FLI format for the Hi-speed is not yet very well documented, it is basically based on the original FLI format with a few new data types. We also support color cameras. But from our experience, if we added a header entry that the
bio-formats FLI reader did not recognize, it would just ignore it. Unless it makes a collision with another key entry. <br class="">
<br class="">
</div>
<div class="">So basically the main issues currently are the Data type and the 2gb File size max. </div>
<div class="">It will become possible to open very big files virtually, right? Because we can easily make files that are 50GB or bigger so it can most of the time never fit the RAM memory.</div>
</div>
</div>
</blockquote>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">About 2GB, I assume you are referring to the issue described in this section of the</div>
<div class="">technical documentation [1]? Briefly, we are routinely dealing with datasets in the</div>
<div class="">GB-TB magnitude so file size per se should not be a problem.</div>
<div class=""><br class="">
</div>
<div class="">Am I correct in assuming you are loading data using the ImageJ/Fiji Bio-Formats</div>
<div class="">Plugin? In that case opening as a virtual stack is definitely the first thing to do. For</div>
<div class="">images where Individual planes exceed 2GB limit (due to dimensions or pixel type),</div>
<div class="">you might need to use the Crop option to load images in tiles rather than whole planes.</div>
<div class="">
<div class=""><br class="">
</div>
<div class="">[1] <a href="https://docs.openmicroscopy.org/bio-formats/5.9.2/about/bug-reporting.html" rel="noreferrer noreferrer" target="_blank" class="">https://docs.openmicroscopy.org/bio-formats/5.9.2/about/bug-reporting.html</a></div>
</div>
<div class=""><br class="">
</div>
<br class="">
<blockquote type="cite" class="">
<div class="">
<div dir="ltr" class="">
<div class="">Regarding compiling Bio-formats, I probably should have given it more time, which I did not had, unfortunately, to have given the manual a better read. What IDE are you using or are you compiling command line?</div>
</div>
</div>
</blockquote>
<div class=""><br class="">
</div>
<div class="">Generally this documentation page is the landing page for everything related to building</div>
<div class="">Bio-Formats from source [2]. In general, people will use either the command-line or an IDE,</div>
<div class="">Eclipse being probably the most popular one. We should be able to offer guidance for both</div>
<div class="">paths. </div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
[2] <a href="https://docs.openmicroscopy.org/bio-formats/5.9.2/developers/building-bioformats.html" rel="noreferrer noreferrer" target="_blank" class="">https://docs.openmicroscopy.org/bio-formats/5.9.2/developers/building-bioformats.html</a> <br class="">
<br class="">
<blockquote type="cite" class="">
<div class="">
<div dir="ltr" class="">
<div dir="ltr" class="">
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<div class="">
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<div class="">I am looking forward to receiving the fix</div>
<div dir="ltr" class=""><br class="">
</div>
<div dir="ltr" class=""><span style="font-size:12.8px" class="">Best regards,</span><br class="">
</div>
<div dir="ltr" class=""><br style="font-size:12.8px" class="">
<span style="font-size:12.8px" class="">Johan Herz, Sales Engineer </span><br style="font-size:12.8px" class="">
<span style="font-size:12.8px" class=""><br class="">
</span></div>
<div dir="ltr" class="">Please visit <a href="http://flim.camera/" rel="noreferrer noreferrer" target="_blank" class="">FLIM.camera</a> for more information about the Toggel.</div>
<div dir="ltr" class=""><span style="font-size:12.8px" class=""><br class="">
</span></div>
<div dir="ltr" class="">
<div dir="ltr" style="font-size:12.8px" class=""><span style="font-size:12.8px" class="">Tel: +31-50-501-8461 | Skype: lambert-</span>johan<br class="">
</div>
<div dir="ltr" style="font-size:12.8px" class=""><span style="font-size:12.8px" class="">Lambert Instruments BV|Leonard Springerlaan 19 (5th floor)|9727 KB Groningen|The Netherlands</span><br style="font-size:12.8px" class="">
<span style="font-size:12.8px" class="">Dutch Chamber of Commerce nr.: 52396940 | </span><a href="http://www.lambertinstruments.com/" style="font-size:12.8px" rel="noreferrer noreferrer" target="_blank" class="">www.lambertinstruments.com</a></div>
</div>
</div>
</div>
</div>
</div>
</div>
<br class="">
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="">Op di 8 jan. 2019 om 18:04 schreef Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" rel="noreferrer noreferrer" target="_blank" class="">s.besson@dundee.ac.uk</a>>:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="">
<div class="">Hi Johan and Aaron,</div>
<div class=""><br class="">
</div>
<div class="">Thanks for making example images available, we will copy them internally for testing purposes.</div>
<div class="">Is an amended version of the technical documentation described the format changes also available?</div>
<div class=""><br class="">
</div>
<div class="">So far we have captured this new variant of the .fli format in the general Bio-Formats backlog [1].</div>
<div class="">In terms of priority, the academically-funded team will primarily focus on next-generation open formats</div>
<div class="">In 2019, starting with the release of Bio-Formats 6 [2]. Although we will not be able to prioritise such work,</div>
<div class="">we will happily review any direct community contribution to update the reader. An alternate possibility solution</div>
<div class="">would be to get in touch with Glencoe Software and commission the reader update.</div>
<div class=""><br class="">
</div>
<div class="">Trying to work in incremental steps and solve the immediate blockers, Johan, could you give us more details</div>
<div class="">into the type of issues you ran into while compiling Bio-Formats?</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">[1] <a href="https://trello.com/c/OGGEzj7X/305-li-flim-12-bit-format" rel="noreferrer noreferrer" target="_blank" class="">https://trello.com/c/OGGEzj7X/305-li-flim-12-bit-format</a></div>
<div class="">[2] <a href="https://blog.openmicroscopy.org/file-formats/community/2018/11/29/ometiffpyramid/" rel="noreferrer noreferrer" target="_blank" class="">https://blog.openmicroscopy.org/file-formats/community/2018/11/29/ometiffpyramid/</a> </div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On 7 Jan 2019, at 09:28, Ponti Aaron <<a href="mailto:aaron.ponti@bsse.ethz.ch" rel="noreferrer noreferrer" target="_blank" class="">aaron.ponti@bsse.ethz.ch</a>> wrote:</div>
<br class="m_-5160481645704919580m_-4377294682811180876gmail-m_-5016623549540082463m_2790263582666838971gmail-m_-3361797864820958579Apple-interchange-newline">
<div class="">
<div class="m_-5160481645704919580m_-4377294682811180876gmail-m_-5016623549540082463m_2790263582666838971gmail-m_-3361797864820958579WordSection1" style="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;text-decoration:none">
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
Hi,<u class=""></u><u class=""></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<u class=""></u> <u class=""></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
Happy new year, everyone! Sorry for the long silence about the FMI issue. I don’t think I will soon find the time to implement support for 12-but FLI files in bio-formats myself. I see that Johan replied to the thread and provided example images. Would you
guys work together to sort out the issue? That’d be great!<u class=""></u><u class=""></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<u class=""></u> <u class=""></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
Thanks a lot!<u class=""></u><u class=""></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
a2<u class=""></u><u class=""></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
<u class=""></u> <u class=""></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif" class="">
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<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<u class=""></u><u class=""></u></span></div>
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<span style="color:rgb(31,73,125)" class="">Software and Data Management Engineer<u class=""></u><u class=""></u></span></div>
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<span lang="DE-CH" style="color:rgb(31,73,125)" class=""><a href="mailto:aaron.ponti@bsse.ethz.ch" style="color:purple;text-decoration:underline" rel="noreferrer noreferrer" target="_blank" class=""><span style="color:rgb(5,99,193)" class="">aaron.ponti@bsse.ethz.ch</span></a><u class=""></u><u class=""></u></span></div>
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<span lang="DE-CH" style="color:rgb(31,73,125)" class="">T: +41 61 387 33 74<u class=""></u><u class=""></u></span></div>
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<span lang="DE-CH" style="color:rgb(31,73,125)" class="">F: +41 61 387 39 93<u class=""></u><u class=""></u></span></div>
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<b class="">From:</b><span class="m_-5160481645704919580m_-4377294682811180876gmail-m_-5016623549540082463m_2790263582666838971gmail-m_-3361797864820958579Apple-converted-space"> </span>Johan Herz <<a href="mailto:johan@lambertinstruments.com" rel="noreferrer noreferrer" target="_blank" class="">johan@lambertinstruments.com</a>><span class="m_-5160481645704919580m_-4377294682811180876gmail-m_-5016623549540082463m_2790263582666838971gmail-m_-3361797864820958579Apple-converted-space"> </span><br class="">
<b class="">Sent:</b><span class="m_-5160481645704919580m_-4377294682811180876gmail-m_-5016623549540082463m_2790263582666838971gmail-m_-3361797864820958579Apple-converted-space"> </span>Mittwoch, 19. Dezember 2018 17:19<br class="">
<b class="">To:</b><span class="m_-5160481645704919580m_-4377294682811180876gmail-m_-5016623549540082463m_2790263582666838971gmail-m_-3361797864820958579Apple-converted-space"> </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" rel="noreferrer noreferrer" target="_blank" class="">ome-users@lists.openmicroscopy.org.uk</a>><br class="">
<b class="">Cc:</b><span class="m_-5160481645704919580m_-4377294682811180876gmail-m_-5016623549540082463m_2790263582666838971gmail-m_-3361797864820958579Apple-converted-space"> </span>Lummen Tom <<a href="mailto:tom.lummen@bsse.ethz.ch" rel="noreferrer noreferrer" target="_blank" class="">tom.lummen@bsse.ethz.ch</a>>;
Ponti Aaron <<a href="mailto:aaron.ponti@bsse.ethz.ch" rel="noreferrer noreferrer" target="_blank" class="">aaron.ponti@bsse.ethz.ch</a>><br class="">
<b class="">Subject:</b><span class="m_-5160481645704919580m_-4377294682811180876gmail-m_-5016623549540082463m_2790263582666838971gmail-m_-3361797864820958579Apple-converted-space"> </span>Re: [ome-users] Support for .FLI files from Capture software (HiCAM
FLUO high-speed camera)<u class=""></u><u class=""></u></div>
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Hello Sebastien,<u class=""></u><u class=""></u></div>
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Thank you for your reply. <u class=""></u><u class=""></u></div>
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I have 2 files, 6 GB each.<u class=""></u><u class=""></u></div>
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They are made with 2 different versions of Capture our Hi-speed recording software. <u class=""></u><u class=""></u></div>
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We make use of the .fli format and we tried to be as compatible with the Bio-formats as possible.<u class=""></u><u class=""></u></div>
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Unfortunately, we could not work around the 12 bit, hence the unsupported data format.<u class=""></u><u class=""></u></div>
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Personally, I have tried to get bio-formats to compile on my one machine, I made a checkout, but I ran in too many problems. It seems that you are planning to have a new release.<u class=""></u><u class=""></u></div>
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Because I wanted to fix the problem of not being able to open files having a filesize bigger than 2 GB. <u class=""></u><u class=""></u></div>
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So could you take this in to account as well? To open our files virtual, FiJi supports this, right?<u class=""></u><u class=""></u></div>
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Is it okay for you if I share the files through Google Drive, as they are too big to upload to your server?<u class=""></u><u class=""></u></div>
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<b class=""><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)" class=""><a href="https://drive.google.com/a/lambertinstruments.com/file/d/1xw43lsucOssXb97ia0JJCCZ9467hV3iO/view?usp=drive_web" style="color:purple;text-decoration:underline" rel="noreferrer noreferrer" target="_blank" class=""><span style="border:1pt none windowtext;padding:0cm;text-decoration:none" class=""><img border="0" id="m_-5160481645704919580m_-4377294682811180876gmail-m_-5016623549540082463m_2790263582666838971gmail-m_-3361797864820958579_x0000_i1025" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png" class=""> </span><span style="color:rgb(17,85,204);border:1pt none windowtext;padding:0cm;text-decoration:none" class="">Recording_Capture_1.1.fli</span></a><u class=""></u><u class=""></u></span></b></div>
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<b class=""><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)" class=""><a href="https://drive.google.com/a/lambertinstruments.com/file/d/19NwEUveiphMxUf9QSjtSHSMBthlaPxqW/view?usp=drive_web" style="color:purple;text-decoration:underline" rel="noreferrer noreferrer" target="_blank" class=""><span style="border:1pt none windowtext;padding:0cm;text-decoration:none" class=""><img border="0" id="m_-5160481645704919580m_-4377294682811180876gmail-m_-5016623549540082463m_2790263582666838971gmail-m_-3361797864820958579_x0000_i1026" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png" class=""> </span><span style="color:rgb(17,85,204);border:1pt none windowtext;padding:0cm;text-decoration:none" class="">Recording_Capture_1.0.4.fli</span></a><u class=""></u><u class=""></u></span></b></div>
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Also have attached a Recording with our New FLIM system, because originally the .fli was for our FLIM system.<u class=""></u><u class=""></u></div>
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Those files are still compatible. So for testing purposes, I included that such that you can make sure it still works.<u class=""></u><u class=""></u></div>
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See attachment.<u class=""></u><u class=""></u></div>
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Please let me know if you have any further questions.<u class=""></u><u class=""></u></div>
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<span style="font-size:9.5pt" class="">Best regards,</span><u class=""></u><u class=""></u></div>
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Johan Herz, Sales Engineer </span><u class=""></u><u class=""></u></p>
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Please visit <a href="http://flim.camera/" style="color:purple;text-decoration:underline" rel="noreferrer noreferrer" target="_blank" class="">FLIM.camera</a> for more information about the Toggel.<u class=""></u><u class=""></u></div>
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<span style="font-size:9.5pt" class="">Tel: +31-50-501-8461 | Skype: lambert-johan<u class=""></u><u class=""></u></span></div>
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<span style="font-size:9.5pt" class="">Lambert Instruments BV|Leonard Springerlaan 19 (5th floor)|9727 KB Groningen|The Netherlands<br class="">
Dutch Chamber of Commerce nr.: 52396940 | <a href="http://www.lambertinstruments.com/" style="color:purple;text-decoration:underline" rel="noreferrer noreferrer" target="_blank" class="">www.lambertinstruments.com</a><u class=""></u><u class=""></u></span></div>
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Op ma 17 dec. 2018 om 15:41 schreef Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" style="color:purple;text-decoration:underline" rel="noreferrer noreferrer" target="_blank" class="">s.besson@dundee.ac.uk</a>>:<u class=""></u><u class=""></u></div>
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Hi Aaron,<span class="m_-5160481645704919580m_-4377294682811180876gmail-m_-5016623549540082463m_2790263582666838971gmail-m_-3361797864820958579Apple-converted-space"> </span><u class=""></u><u class=""></u></div>
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On 14 Dec 2018, at 10:00, Ponti Aaron <<a href="mailto:aaron.ponti@bsse.ethz.ch" style="color:purple;text-decoration:underline" rel="noreferrer noreferrer" target="_blank" class="">aaron.ponti@bsse.ethz.ch</a>> wrote:<u class=""></u><u class=""></u></div>
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Hello,<u class=""></u><u class=""></u></div>
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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:purple;text-decoration:underline" rel="noreferrer noreferrer" target="_blank" class=""><span style="color:rgb(149,79,114)" class="">https://github.com/openmicroscopy/bioformats/blob/develop/components/formats-gpl/src/loci/formats/in/LiFlimReader.java</span></a>)
does not seem to support 12-bit intensities.<span class="m_-5160481645704919580m_-4377294682811180876gmail-m_-5016623549540082463m_2790263582666838971gmail-m_-3361797864820958579Apple-converted-space"> </span><u class=""></u><u class=""></u></div>
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From the internal specification of the LI-FLIM file format which we used for the reader [1]:<u class=""></u><u class=""></u></div>
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"The datatype key can have one of the following 8 values: UINT8, INT8, UINT16, INT16,<u class=""></u><u class=""></u></div>
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UINT32, INT32, REAL32 or REAL64.”<u class=""></u><u class=""></u></div>
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A file that would use UINT12 would probably be a new variant of the file format for which we<u class=""></u><u class=""></u></div>
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have currently neither a format specification nor representative samples<u class=""></u><u class=""></u></div>
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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).<u class=""></u><u class=""></u></div>
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Understood. This would be consistent with the pixel type issue reported above i.e. that could<u class=""></u><u class=""></u></div>
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indeed reflect an internal layout different from the one Bio-Formats is expecting..<u class=""></u><u class=""></u></div>
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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.<u class=""></u><u class=""></u></div>
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Would you be interested in adding support for these files to bio-formats? We have example files that we could upload.<u class=""></u><u class=""></u></div>
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Over the past years, we have been working on ways to have more sustainable support for new file<u class=""></u><u class=""></u></div>
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formats including any variants of existing file formats. We published a blog post summarizing our<u class=""></u><u class=""></u></div>
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experience a few years ago [2] and since then more manufacturers have been engaging in this<u class=""></u><u class=""></u></div>
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process.<u class=""></u><u class=""></u></div>
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Have you been in touch with Lambert Instruments to report this issue? Are they aware that the latest files<u class=""></u><u class=""></u></div>
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produced by their software are no longer readable by Bio-Formats and any software based upon it?<u class=""></u><u class=""></u></div>
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Representative samples allowing to reproduce the issue are always welcome. Ideally public samples licensed<u class=""></u><u class=""></u></div>
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under CC-BY license [3] are the most effective way to help spontaneous or sponsored contributions to the<u class=""></u><u class=""></u></div>
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project and facilitate both the immediate software work as well as the long-term maintenance.<u class=""></u><u class=""></u></div>
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You can upload datasets under 2GB to our QA system [4] and we can provide FTP credentials for large samples.<u class=""></u><u class=""></u></div>
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Best,<u class=""></u><u class=""></u></div>
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Sebastien<u class=""></u><u class=""></u></div>
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[1] <a href="https://docs.openmicroscopy.org/bio-formats/5.9.2/formats/lambert-instruments-flim.html" style="color:purple;text-decoration:underline" rel="noreferrer noreferrer" target="_blank" class="">https://docs.openmicroscopy.org/bio-formats/5.9.2/formats/lambert-instruments-flim.html</a><u class=""></u><u class=""></u></div>
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[2] <a href="https://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/" style="color:purple;text-decoration:underline" rel="noreferrer noreferrer" target="_blank" class="">https://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/</a><u class=""></u><u class=""></u></div>
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[3] <a href="https://downloads.openmicroscopy.org/images/" style="color:purple;text-decoration:underline" rel="noreferrer noreferrer" target="_blank" class="">https://downloads.openmicroscopy.org/images/</a><u class=""></u><u class=""></u></div>
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[4] <a href="http://qa.openmicroscopy.org.uk/qa/upload/" style="color:purple;text-decoration:underline" rel="noreferrer noreferrer" target="_blank" class="">http://qa.openmicroscopy.org.uk/qa/upload/</a><u class=""></u><u class=""></u></div>
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Thanks a lot,<u class=""></u><u class=""></u></div>
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a2<u class=""></u><u class=""></u></div>
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<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</span><u class=""></u><u class=""></u></div>
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<span style="color:rgb(31,73,125)" class="">Software and Data Management Engineer</span><u class=""></u><u class=""></u></div>
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<span style="color:rgb(31,73,125)" class="">Image Analysis Specialist</span><u class=""></u><u class=""></u></div>
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<span style="color:rgb(31,73,125)" class="">Single Cell Facility</span><u class=""></u><u class=""></u></div>
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<span style="color:rgb(31,73,125)" class="">Department of Biosystems Science and Engineering (D-BSSE)</span><u class=""></u><u class=""></u></div>
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<span lang="DE-CH" style="color:rgb(31,73,125)" class="">ETH Zürich</span><u class=""></u><u class=""></u></div>
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<span lang="DE-CH" style="color:rgb(31,73,125)" class="">Office 2.30</span><u class=""></u><u class=""></u></div>
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<span lang="DE-CH" style="color:rgb(31,73,125)" class="">Mattenstrasse 26</span><u class=""></u><u class=""></u></div>
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<span lang="DE-CH" style="color:rgb(31,73,125)" class="">4058 Basel, Switzerland</span><u class=""></u><u class=""></u></div>
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<span lang="DE-CH" style="color:rgb(31,73,125)" class=""><a href="mailto:aaron.ponti@bsse.ethz.ch" style="color:purple;text-decoration:underline" rel="noreferrer noreferrer" target="_blank" class=""><span style="color:rgb(5,99,193)" class="">aaron.ponti@bsse.ethz.ch</span></a></span><u class=""></u><u class=""></u></div>
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<span lang="DE-CH" style="color:rgb(31,73,125)" class="">T: +41 61 387 33 74</span><u class=""></u><u class=""></u></div>
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<span lang="DE-CH" style="color:rgb(31,73,125)" class="">F: +41 61 387 39 93</span><u class=""></u><u class=""></u></div>
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<span style="font-size:9pt;font-family:Helvetica,sans-serif" class="">_______________________________________________<br class="">
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<span style="font-size:10pt" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span><u class=""></u><u class=""></u></div>
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<span style="font-size:10pt" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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<span style="font-size:10pt" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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<span style="font-size:10pt" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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<span style="font-size:10pt" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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