[ome-devel] czbmi

[Lai Ghee Hwee (Dr)]

Thanks Petr for the trello card,

I’ll try to raise the issue when I see zeiss support.
Much appreciated for the possible courses of action! I’ll study and see how best to push efforts — it makes good sense for me to look for more folks that face the same problem with multi-block acquisition.

Sincerely,
Ghee Hwee

On 15 Mar 2019, at 5:22 PM, Petr Walczysko (Staff) <p.walczysko at dundee.ac.uk<mailto:p.walczysko at dundee.ac.uk>> wrote:

Dear Ghee

We have created a trello card https://trello.com/c/j9FCLOZu/359-czbmi-new-structured-directories-czi-format to deal with this matter in Bio-Formats.
Thank you very much for your suggestions and interest.
This is clearly a “yet-another-format” problem which we had to deal with many times before.
One option is to support the effort by submitting Pull Requests to the Bio-Formats reader repository by following the instructions outlined at https://docs.openmicroscopy.org/latest/bio-formats6.0/developers/.
More precisely, the relevant chapter is https://docs.openmicroscopy.org/latest/bio-formats6.0/developers/reader-guide.html .
Another option is to engage directly with the manufacturers and ask them to commission the work. Please see the relevant bloghttp://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/ if you want to pursue this course of action. This approach is more likely to succeed if you join forces with other colleagues using the same format.

Hope this helps.

Thank you once more.

All the best

Petr

OME Team




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

The University of Dundee is a registered Scottish Charity, No: SC015096

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