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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">"Lai Ghee Hwee (Dr)" <ghlai@ntu.edu.sg><br>
<b>Date: </b>Wednesday, 13 March 2019 at 09:35<br>
<b>To: </b>"Petr Walczysko (Staff)" <p.walczysko@dundee.ac.uk><br>
<b>Cc: </b>"Jean-Marie Burel (Staff)" <j.burel@dundee.ac.uk>, Talgat Sailov <tsailov@ntu.edu.sg><br>
<b>Subject: </b>Re: Thank you :) <o:p></o:p></span></p>
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<p class="MsoNormal">Certainly, thanks for asking! <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Stay warm,<o:p></o:p></p>
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<p class="MsoNormal">Ghee Hwee<o:p></o:p></p>
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<p class="MsoNormal">On 13 Mar 2019, at 5:32 PM, Petr Walczysko (Staff) <<a href="mailto:p.walczysko@dundee.ac.uk">p.walczysko@dundee.ac.uk</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">Dear Ghee,<o:p></o:p></p>
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<p class="MsoNormal">Thank you very much for this precise description.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Would you please be happy for me to forward it to ome-devel distribution list,<o:p></o:p></p>
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<p class="MsoNormal">so that the whole OME Team can discuss and contribute ?<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Thank you once more, also for your good wishes.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">All the best<o:p></o:p></p>
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<p class="MsoNormal">Petr<o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt">From:<span class="apple-converted-space"> </span></span></b><span style="font-size:12.0pt">"Lai Ghee Hwee (Dr)" <<a href="mailto:ghlai@ntu.edu.sg"><span style="color:purple">ghlai@ntu.edu.sg</span></a>><br>
<b>Date:<span class="apple-converted-space"> </span></b>Wednesday, 13 March 2019 at 06:18<br>
<b>To:<span class="apple-converted-space"> </span></b>"Jean-Marie Burel (Staff)" <<a href="mailto:j.burel@dundee.ac.uk"><span style="color:purple">j.burel@dundee.ac.uk</span></a>>, "Petr Walczysko (Staff)" <<a href="mailto:p.walczysko@dundee.ac.uk"><span style="color:purple">p.walczysko@dundee.ac.uk</span></a>><br>
<b>Cc:<span class="apple-converted-space"> </span></b>Talgat Sailov <<a href="mailto:tsailov@ntu.edu.sg"><span style="color:purple">tsailov@ntu.edu.sg</span></a>><br>
<b>Subject:<span class="apple-converted-space"> </span></b>Re: Thank you :)<span class="apple-converted-space"> </span></span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Dear Jean-Marie and Petr,<span class="apple-converted-space"> </span><o:p></o:p></p>
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<p class="MsoNormal">Glad to hear you all are safely back, stay warm!<o:p></o:p></p>
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<p class="MsoNormal">Thanks for asking about the czi structure for multi-block acquisition on Zeiss.<o:p></o:p></p>
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<p class="MsoNormal">I found a smaller test set and zipped it up for sharing (<a href="https://www.dropbox.com/s/3wjxqd2i66zau2s/Archive.zip"><span style="color:purple">https://www.dropbox.com/s/3wjxqd2i66zau2s/Archive.zip</span></a> , approximately 57MB).<o:p></o:p></p>
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<p class="MsoNormal">The structure of the output from zeiss is as below:<o:p></o:p></p>
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<p class="MsoNormal" style="background:#212121"><span style="font-size:8.5pt;font-family:Menlo;color:#D6D6D6">├── PA01gfp_PF5mScarlet-1.czi</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:#212121"><span style="font-size:8.5pt;font-family:Menlo;color:#D6D6D6">│ ├── PA01gfp_PF5mScarlet-1.czmbi</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:#212121"><span style="font-size:8.5pt;font-family:Menlo;color:#D6D6D6">│ ├── PA01gfp_PF5mScarlet-1_AcquisitionBlock1.czi</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:#212121"><span style="font-size:8.5pt;font-family:Menlo;color:#D6D6D6">│ │ └── PA01gfp_PF5mScarlet-1_AcquisitionBlock1_pt1.czi</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:#212121"><span style="font-size:8.5pt;font-family:Menlo;color:#D6D6D6">│ └── PA01gfp_PF5mScarlet-1_AcquisitionBlock2.czi</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:#212121"><span style="font-size:8.5pt;font-family:Menlo;color:#D6D6D6">│ └── PA01gfp_PF5mScarlet-1_AcquisitionBlock2_pt2.czi</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:#212121"><span style="font-size:8.5pt;font-family:Menlo;color:#D6D6D6">└── zen\ blue.JPG</span><o:p></o:p></p>
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<p class="MsoNormal">1. folder named with .czi<o:p></o:p></p>
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<p class="MsoNormal">2. master file to open in zen blue is the .czmbi<o:p></o:p></p>
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<p class="MsoNormal">3. each block has its own folder with .czi end<o:p></o:p></p>
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<p class="MsoNormal">4. first block is 3 channel (3 x 2048 x 2048) for brightfield + red + green<o:p></o:p></p>
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<p class="MsoNormal">5. second block is a timelapse of brightfield (7 x 2048 x 2048)<o:p></o:p></p>
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<p class="MsoNormal">Picture below is how it looks on zen blue, when i open the czmbi file — it understands the 2 block structure and has 8 timepoints, the first with 3 channels and the other 7 in brightfield only. I stopped this after one loop, so usually
each folder block would have many more czi files for different timepoints (10 to hundreds for testing examples).<o:p></o:p></p>
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<p class="MsoNormal"><image001.jpg><o:p></o:p></p>
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<p class="MsoNormal">If omero allows upload of folders, i can keep the raw data intact without flattening it (zeiss won’t read after flattening). It would be great too if omero allows upload of files it can’t recognize (or won’t open) — the czmbi file would
be rejected, or a README.md/txt within the folder would be great for bookkeeping. This would allow the same folder structure on both the local machine and “what’s viewable” on the omero server, rather than two slightly different formats which may be fragile
as projects change hands over time perhaps? Not sure how difficult it would be, so thanks for thinking about it. Maybe along the same spirit as <a href="https://cloud.google.com/storage/docs/gsutil/addlhelp/HowSubdirectoriesWork"><span style="color:purple">how
flat namespace storage buckets mimic nested directories</span></a> by treating the entire directory path with “/“ characters as the object name (but I’m not sure if it affects windows users with 260 char limit).<o:p></o:p></p>
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<p class="MsoNormal">Ghee Hwee<o:p></o:p></p>
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<p class="MsoNormal">On 13 Mar 2019, at 1:00 PM, Talgat Sailov <<a href="mailto:tsailov@ntu.edu.sg"><span style="color:purple">tsailov@ntu.edu.sg</span></a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif">From:</span></b><span class="apple-converted-space"><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif"> </span></span><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif">Jean-Marie
Burel (Staff) [<a href="mailto:j.burel@dundee.ac.uk"><span style="color:purple">mailto:j.burel@dundee.ac.uk</span></a>]<span class="apple-converted-space"> </span><br>
<b>Sent:</b><span class="apple-converted-space"> </span>Monday, March 11, 2019 10:00 PM<br>
<b>To:</b><span class="apple-converted-space"> </span>Talgat Sailov; Petr Walczysko (Staff)<br>
<b>Cc:</b><span class="apple-converted-space"> </span>June Matthew (Staff); Jason Swedlow (Staff)<br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: Thank you :)<span class="apple-converted-space"> </span></span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt">Dear Tailgate</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt">We made it back safely to Scotland. 2C when we went off the plane this morning. Our body was not ready for such welcome.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt">I have updated Day 2 of the workshop following the demo request of to useTrackMate and OMERO during the second day</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt"><a href="http://downloads.openmicroscopy.org/presentations/2019/Singapore/Singapore_2019_Day2.pdf"><span style="color:purple">http://downloads.openmicroscopy.org/presentations/2019/Singapore/Singapore_2019_Day2.pdf</span></a></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt">John and your colleague who shares an office with you (sorry I forgot his name) were interested in that section.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt">Also will it be possible to have some sample data for the czi flavour that could not be imported (combination of czi files)? </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt">We will sort out the receipts in the coming days and send you the document</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt">Thanks for hosting us</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt">We really enjoyed our stay.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt">Best</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt">Jmarie</span><o:p></o:p></p>
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<p class="MsoNormal"><b>From:<span class="apple-converted-space"> </span></b>Talgat Sailov <<a href="mailto:tsailov@ntu.edu.sg"><span style="color:purple">tsailov@ntu.edu.sg</span></a>><br>
<b>Date:<span class="apple-converted-space"> </span></b>Monday, 11 March 2019 at 09:27<br>
<b>To:<span class="apple-converted-space"> </span></b>jmarie burel <<a href="mailto:j.burel@dundee.ac.uk"><span style="color:purple">j.burel@dundee.ac.uk</span></a>>, "Petr Walczysko (Staff)" <<a href="mailto:p.walczysko@dundee.ac.uk"><span style="color:purple">p.walczysko@dundee.ac.uk</span></a>><br>
<b>Cc:<span class="apple-converted-space"> </span></b>"June Matthew (Staff)" <<a href="mailto:J.Matthew@dundee.ac.uk"><span style="color:purple">J.Matthew@dundee.ac.uk</span></a>>, "Jason Swedlow (Staff)" <<a href="mailto:j.r.swedlow@dundee.ac.uk"><span style="color:purple">j.r.swedlow@dundee.ac.uk</span></a>><br>
<b>Subject:<span class="apple-converted-space"> </span></b>Thank you :)<span class="apple-converted-space"> </span><o:p></o:p></p>
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<p class="MsoNormal">Dear Jean-Marie and Petr,<span class="apple-converted-space"> </span><o:p></o:p></p>
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<p class="MsoNormal">Hope you landed safely! On behalf of SCELSE I would like to thank you for conducting a productive workshop in Singapore. We have had great feedback from our users who attended the hands-on workshop.<o:p></o:p></p>
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<p class="MsoNormal">Some of the photo highlights from your visit to Singapore <a href="https://we.tl/t-YW8u9gn5KG"><span style="color:purple">https://we.tl/t-YW8u9gn5KG</span></a> (expires in 7 days). May I also kindly request to send me your scanned receipts
accumulated during your stay in NTU, please?<o:p></o:p></p>
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<p class="MsoNormal">Thanks again,<o:p></o:p></p>
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<p class="MsoNormal">Best wishes,<span class="apple-converted-space"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:11.55pt"><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#6D6E71">Talgat SAILOV (Mr)</span></b><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:11.55pt"><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#6D6E71">Microscopy Officer</span><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:11.55pt"><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#6D6E71">60 Nanyang Drive, SBS-01N-27, Singapore 637551</span><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:11.55pt"><b><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#6D6E71">T:</span></b><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#6D6E71"> +65 6592 7901 | <b>F:</b> +65 6315 6751 | <b>E:</b> </span><span style="font-size:9.0pt;font-family:"Arial",sans-serif"><a href="mailto:tsailov@ntu.edu.sg"><span style="color:purple">tsailov@ntu.edu.sg</span></a><span class="apple-converted-space"><span style="color:#6D6E71"> </span></span><span style="color:#6D6E71">| </span></span><a href="http://www.scelse.sg/"><b><span style="font-size:9.0pt;font-family:"Arial",sans-serif;color:#6D6E71;text-decoration:none">www.scelse.sg</span></b></a><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:gray">CONFIDENTIALITY: This email is intended solely for the person(s) named and may be confidential and/or privileged. If you are not the intended recipient, please delete
it, notify us and do not copy, use, or disclose its contents.<br>
Towards a sustainable earth: Print only when necessary. Thank you.</span><o:p></o:p></p>
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</span><span style="font-size:10.0pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span><o:p></o:p></p>
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</span><span style="font-size:10.0pt;font-family:Helvetica">The University of Dundee is a registered Scottish Charity, No: SC015096</span><o:p></o:p></p>
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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