[ome-devel] czbmi

Wed Mar 13 09:39:05 GMT 2019

From: "Lai Ghee Hwee (Dr)" <ghlai at ntu.edu.sg>
Date: Wednesday, 13 March 2019 at 09:35
To: "Petr Walczysko (Staff)" <p.walczysko at dundee.ac.uk>
Cc: "Jean-Marie Burel (Staff)" <j.burel at dundee.ac.uk>, Talgat Sailov <tsailov at ntu.edu.sg>
Subject: Re: Thank you :)

Certainly, thanks for asking!

Stay warm,
Ghee Hwee

On 13 Mar 2019, at 5:32 PM, Petr Walczysko (Staff) <p.walczysko at dundee.ac.uk<mailto:p.walczysko at dundee.ac.uk>> wrote:

Dear Ghee,
Thank you very much for this precise description.

Would you please be happy for me to forward it to ome-devel distribution list,
so that the whole OME Team can discuss and contribute ?

Thank you once more, also for your good wishes.

All the best

Petr

From: "Lai Ghee Hwee (Dr)" <ghlai at ntu.edu.sg<mailto:ghlai at ntu.edu.sg>>
Date: Wednesday, 13 March 2019 at 06:18
To: "Jean-Marie Burel (Staff)" <j.burel at dundee.ac.uk<mailto:j.burel at dundee.ac.uk>>, "Petr Walczysko (Staff)" <p.walczysko at dundee.ac.uk<mailto:p.walczysko at dundee.ac.uk>>
Cc: Talgat Sailov <tsailov at ntu.edu.sg<mailto:tsailov at ntu.edu.sg>>
Subject: Re: Thank you :)

Dear Jean-Marie and Petr,

Glad to hear you all are safely back, stay warm!

Thanks for asking about the czi structure for multi-block acquisition on Zeiss.
I found a smaller test set and zipped it up for sharing (https://www.dropbox.com/s/3wjxqd2i66zau2s/Archive.zip , approximately 57MB).

The structure of the output from zeiss is as below:

├── PA01gfp_PF5mScarlet-1.czi
│   ├── PA01gfp_PF5mScarlet-1.czmbi
│   ├── PA01gfp_PF5mScarlet-1_AcquisitionBlock1.czi
│   │   └── PA01gfp_PF5mScarlet-1_AcquisitionBlock1_pt1.czi
│   └── PA01gfp_PF5mScarlet-1_AcquisitionBlock2.czi
│       └── PA01gfp_PF5mScarlet-1_AcquisitionBlock2_pt2.czi
└── zen\ blue.JPG

1. folder named with .czi
2. master file to open in zen blue is the .czmbi
3. each block has its own folder with .czi end
4. first block is 3 channel  (3 x 2048 x 2048) for brightfield + red + green
5. second block is a timelapse of brightfield (7 x 2048 x 2048)

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).

<image001.jpg>

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 how flat namespace storage buckets mimic nested directories<https://cloud.google.com/storage/docs/gsutil/addlhelp/HowSubdirectoriesWork> 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).

Ghee Hwee

On 13 Mar 2019, at 1:00 PM, Talgat Sailov <tsailov at ntu.edu.sg<mailto:tsailov at ntu.edu.sg>> wrote:

From: Jean-Marie Burel (Staff) [mailto:j.burel at dundee.ac.uk]
Sent: Monday, March 11, 2019 10:00 PM
To: Talgat Sailov; Petr Walczysko (Staff)
Cc: June Matthew (Staff); Jason Swedlow (Staff)
Subject: Re: Thank you :)

Dear Tailgate

We made it back safely to Scotland. 2C when we went off the plane this morning. Our body was not ready for such welcome.
I have updated Day 2 of the workshop following the demo request of to useTrackMate and OMERO during the second day
http://downloads.openmicroscopy.org/presentations/2019/Singapore/Singapore_2019_Day2.pdf
John and your colleague who shares an office with you (sorry I forgot his name) were interested in that section.

Also will it be possible to have some sample data for the czi flavour that could not be imported (combination of czi files)?

We will sort out the receipts in the coming days and send you the document

Thanks for hosting us
We really enjoyed our stay.

Best

Jmarie

From: Talgat Sailov <tsailov at ntu.edu.sg<mailto:tsailov at ntu.edu.sg>>
Date: Monday, 11 March 2019 at 09:27
To: jmarie burel <j.burel at dundee.ac.uk<mailto:j.burel at dundee.ac.uk>>, "Petr Walczysko (Staff)" <p.walczysko at dundee.ac.uk<mailto:p.walczysko at dundee.ac.uk>>
Cc: "June Matthew (Staff)" <J.Matthew at dundee.ac.uk<mailto:J.Matthew at dundee.ac.uk>>, "Jason Swedlow (Staff)" <j.r.swedlow at dundee.ac.uk<mailto:j.r.swedlow at dundee.ac.uk>>
Subject: Thank you :)

Dear Jean-Marie and Petr,

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.

Some of the photo highlights from your visit to Singapore https://we.tl/t-YW8u9gn5KG (expires in 7 days). May I also kindly request to send me your scanned receipts accumulated during your stay in NTU, please?

Thanks again,
Best wishes,

Talgat SAILOV (Mr)
Microscopy Officer

60 Nanyang Drive, SBS-01N-27, Singapore 637551
T: +65 6592 7901 | F: +65 6315 6751 | E: tsailov at ntu.edu.sg<mailto:tsailov at ntu.edu.sg> | www.scelse.sg<http://www.scelse.sg/>

[cid:image001.jpg at 01D189A9.41868BB0]           [cid:image002.jpg at 01D189A9.41868BB0]

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