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<div class="">Hi Johan and Aaron,</div>
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<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>
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<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>
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<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>
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<div class="">Best,</div>
<div class="">Sebastien</div>
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<div class="">[1] <a href="https://trello.com/c/OGGEzj7X/305-li-flim-12-bit-format" 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/" class="">https://blog.openmicroscopy.org/file-formats/community/2018/11/29/ometiffpyramid/</a> </div>
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<div class="">On 7 Jan 2019, at 09:28, Ponti Aaron <<a href="mailto:aaron.ponti@bsse.ethz.ch" class="">aaron.ponti@bsse.ethz.ch</a>> wrote:</div>
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Hi,<o:p class=""></o:p></div>
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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!<o:p class=""></o:p></div>
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Thanks a lot!<o:p class=""></o:p></div>
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a2<o:p class=""></o:p></div>
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<span style="color: rgb(31, 73, 125);" class="">Dr. Aaron Ponti<o:p class=""></o:p></span></div>
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<span style="color: rgb(31, 73, 125);" class="">Software and Data Management Engineer<o:p class=""></o:p></span></div>
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<span style="color: rgb(31, 73, 125);" class="">Image Analysis Specialist<o:p class=""></o:p></span></div>
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<span style="color: rgb(31, 73, 125);" class="">Single Cell Facility<o:p class=""></o:p></span></div>
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<span style="color: rgb(31, 73, 125);" class="">Department of Biosystems Science and Engineering (D-BSSE)<o:p class=""></o:p></span></div>
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<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">ETH Zürich<o:p class=""></o:p></span></div>
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<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">Office 2.30<o:p class=""></o:p></span></div>
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<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">Mattenstrasse 26<o:p class=""></o:p></span></div>
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<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">4058 Basel, Switzerland<o:p class=""></o:p></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;" class=""><span style="color: rgb(5, 99, 193);" class="">aaron.ponti@bsse.ethz.ch</span></a><o:p class=""></o:p></span></div>
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<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">T: +41 61 387 33 74<o:p class=""></o:p></span></div>
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<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">F: +41 61 387 39 93<o:p class=""></o:p></span></div>
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<b class="">From:</b><span class="Apple-converted-space"> </span>Johan Herz <<a href="mailto:johan@lambertinstruments.com" class="">johan@lambertinstruments.com</a>><span class="Apple-converted-space"> </span><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Mittwoch, 19. Dezember 2018 17:19<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a>><br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span>Lummen Tom <<a href="mailto:tom.lummen@bsse.ethz.ch" class="">tom.lummen@bsse.ethz.ch</a>>; Ponti Aaron <<a href="mailto:aaron.ponti@bsse.ethz.ch" class="">aaron.ponti@bsse.ethz.ch</a>><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ome-users] Support for .FLI files from Capture software (HiCAM FLUO high-speed camera)<o:p class=""></o:p></div>
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Hello Sebastien,<o:p class=""></o:p></div>
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Thank you for your reply. <o:p class=""></o:p></div>
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I have 2 files, 6 GB each.<o:p class=""></o:p></div>
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They are made with 2 different versions of Capture our Hi-speed recording software. <o:p class=""></o:p></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.<o:p class=""></o:p></div>
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Unfortunately, we could not work around the 12 bit, hence the unsupported data format.<o:p class=""></o:p></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.<o:p class=""></o:p></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. <o:p class=""></o:p></div>
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So could you take this in to account as well? To open our files virtual, FiJi supports this, right?<o:p class=""></o:p></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?<o:p class=""></o:p></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" target="_blank" style="color: purple; text-decoration: underline;" class=""><span style="border: 1pt none windowtext; padding: 0cm; text-decoration: none;" class=""><img border="0" id="_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><o:p class=""></o:p></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" target="_blank" style="color: purple; text-decoration: underline;" class=""><span style="border: 1pt none windowtext; padding: 0cm; text-decoration: none;" class=""><img border="0" id="_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><o:p class=""></o:p></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.<o:p class=""></o:p></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.<o:p class=""></o:p></div>
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See attachment.<o:p class=""></o:p></div>
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Please let me know if you have any further questions.<o:p class=""></o:p></div>
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<span style="font-size: 9.5pt;" class="">Best regards,</span><o:p class=""></o:p></div>
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Johan Herz, Sales Engineer </span><o:p class=""></o:p></p>
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Please visit <a href="http://flim.camera/" target="_blank" style="color: purple; text-decoration: underline;" class="">FLIM.camera</a> for more information about the Toggel.<o:p class=""></o:p></div>
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<span style="font-size: 9.5pt;" class="">Tel: +31-50-501-8461 | Skype: lambert-johan<o:p class=""></o:p></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/" target="_blank" style="color: purple; text-decoration: underline;" class="">www.lambertinstruments.com</a><o:p class=""></o:p></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;" class="">s.besson@dundee.ac.uk</a>>:<o:p class=""></o:p></div>
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Hi Aaron,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
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On 14 Dec 2018, at 10:00, Ponti Aaron <<a href="mailto:aaron.ponti@bsse.ethz.ch" target="_blank" style="color: purple; text-decoration: underline;" class="">aaron.ponti@bsse.ethz.ch</a>> wrote:<o:p class=""></o:p></div>
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Hello,<o:p class=""></o:p></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" target="_blank" style="color: purple; text-decoration: underline;" 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="Apple-converted-space"> </span><o:p class=""></o:p></div>
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From the internal specification of the LI-FLIM file format which we used for the reader [1]:<o:p class=""></o:p></div>
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"The datatype key can have one of the following 8 values: UINT8, INT8, UINT16, INT16,<o:p class=""></o:p></div>
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UINT32, INT32, REAL32 or REAL64.”<o:p class=""></o:p></div>
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A file that would use UINT12 would probably be a new variant of the file format for which we<o:p class=""></o:p></div>
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have currently neither a format specification nor representative samples<o:p class=""></o:p></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).<o:p class=""></o:p></div>
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Understood. This would be consistent with the pixel type issue reported above i.e. that could<o:p class=""></o:p></div>
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indeed reflect an internal layout different from the one Bio-Formats is expecting..<o:p class=""></o:p></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.<o:p class=""></o:p></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.<o:p class=""></o:p></div>
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Over the past years, we have been working on ways to have more sustainable support for new file<o:p class=""></o:p></div>
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formats including any variants of existing file formats. We published a blog post summarizing our<o:p class=""></o:p></div>
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experience a few years ago [2] and since then more manufacturers have been engaging in this<o:p class=""></o:p></div>
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process.<o:p class=""></o:p></div>
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Have you been in touch with Lambert Instruments to report this issue? Are they aware that the latest files<o:p class=""></o:p></div>
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produced by their software are no longer readable by Bio-Formats and any software based upon it?<o:p class=""></o:p></div>
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Representative samples allowing to reproduce the issue are always welcome. Ideally public samples licensed<o:p class=""></o:p></div>
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under CC-BY license [3] are the most effective way to help spontaneous or sponsored contributions to the<o:p class=""></o:p></div>
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project and facilitate both the immediate software work as well as the long-term maintenance.<o:p class=""></o:p></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.<o:p class=""></o:p></div>
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Best,<o:p class=""></o:p></div>
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Sebastien<o:p class=""></o:p></div>
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[1] <a href="https://docs.openmicroscopy.org/bio-formats/5.9.2/formats/lambert-instruments-flim.html" target="_blank" style="color: purple; text-decoration: underline;" class="">https://docs.openmicroscopy.org/bio-formats/5.9.2/formats/lambert-instruments-flim.html</a><o:p class=""></o:p></div>
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[2] <a href="https://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/" target="_blank" style="color: purple; text-decoration: underline;" class="">https://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/</a><o:p class=""></o:p></div>
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[3] <a href="https://downloads.openmicroscopy.org/images/" target="_blank" style="color: purple; text-decoration: underline;" class="">https://downloads.openmicroscopy.org/images/</a><o:p class=""></o:p></div>
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[4] <a href="http://qa.openmicroscopy.org.uk/qa/upload/" target="_blank" style="color: purple; text-decoration: underline;" class="">http://qa.openmicroscopy.org.uk/qa/upload/</a><o:p class=""></o:p></div>
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Thanks a lot,<o:p class=""></o:p></div>
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a2<o:p class=""></o:p></div>
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<span style="color: rgb(31, 73, 125);" class="">Dr. Aaron Ponti</span><o:p class=""></o:p></div>
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<span style="color: rgb(31, 73, 125);" class="">Software and Data Management Engineer</span><o:p class=""></o:p></div>
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<span style="color: rgb(31, 73, 125);" class="">Image Analysis Specialist</span><o:p class=""></o:p></div>
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<span style="color: rgb(31, 73, 125);" class="">Single Cell Facility</span><o:p class=""></o:p></div>
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<span style="color: rgb(31, 73, 125);" class="">Department of Biosystems Science and Engineering (D-BSSE)</span><o:p class=""></o:p></div>
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<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">ETH Zürich</span><o:p class=""></o:p></div>
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<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">Office 2.30</span><o:p class=""></o:p></div>
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<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">Mattenstrasse 26</span><o:p class=""></o:p></div>
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<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">4058 Basel, Switzerland</span><o:p class=""></o:p></div>
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<span lang="DE-CH" style="color: rgb(31, 73, 125);" class=""><a href="mailto:aaron.ponti@bsse.ethz.ch" target="_blank" style="color: purple; text-decoration: underline;" class=""><span style="color: rgb(5, 99, 193);" class="">aaron.ponti@bsse.ethz.ch</span></a></span><o:p class=""></o:p></div>
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<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">T: +41 61 387 33 74</span><o:p class=""></o:p></div>
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<span lang="DE-CH" style="color: rgb(31, 73, 125);" class="">F: +41 61 387 39 93</span><o:p class=""></o:p></div>
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