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Thanks Petr for the trello card,
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<div class="">I’ll try to raise the issue when I see zeiss support.</div>
<div class="">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.</div>
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<div class="">Sincerely,</div>
<div class="">Ghee Hwee<br class="">
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<div class="">On 15 Mar 2019, at 5:22 PM, Petr Walczysko (Staff) <<a href="mailto:p.walczysko@dundee.ac.uk" class="">p.walczysko@dundee.ac.uk</a>> wrote:</div>
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<span class="" style="font-family:Arial,sans-serif">Dear Ghee</span></div>
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<span class="" style="font-family:Arial,sans-serif">We have created a trello card<span class="Apple-converted-space"> </span></span><a href="https://trello.com/c/j9FCLOZu/359-czbmi-new-structured-directories-czi-format" class="" style="color:purple; text-decoration:underline"><span class="" style="font-family:Arial,sans-serif; color:rgb(17,85,204)">https://trello.com/c/j9FCLOZu/359-czbmi-new-structured-directories-czi-format</span></a><span class="" style="font-family:Arial,sans-serif"><span class="Apple-converted-space"> </span>to
deal with this matter in Bio-Formats.</span></div>
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<span class="" style="font-family:Arial,sans-serif">Thank you very much for your suggestions and interest.</span></div>
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<span class="" style="font-family:Arial,sans-serif">This is clearly a “yet-another-format” problem which we had to deal with many times before.</span></div>
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<span class="" style="font-family:Arial,sans-serif">One option is to support the effort by submitting Pull Requests to the Bio-Formats reader repository by following the instructions outlined at<span class="Apple-converted-space"> </span></span><a href="https://docs.openmicroscopy.org/latest/bio-formats6.0/developers/" class="" style="color:purple; text-decoration:underline"><span class="" style="font-family:Arial,sans-serif; color:rgb(17,85,204)">https://docs.openmicroscopy.org/latest/bio-formats6.0/developers/</span></a><span class="" style="font-family:Arial,sans-serif">.</span></div>
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<span class="" style="font-family:Arial,sans-serif">More precisely, the relevant chapter is<span class="Apple-converted-space"> </span></span><a href="https://docs.openmicroscopy.org/latest/bio-formats6.0/developers/reader-guide.html" class="" style="color:purple; text-decoration:underline"><span class="" style="font-family:Arial,sans-serif; color:rgb(17,85,204)">https://docs.openmicroscopy.org/latest/bio-formats6.0/developers/reader-guide.html</span></a><span class="" style="font-family:Arial,sans-serif"><span class="Apple-converted-space"> </span>.</span></div>
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<span class="" style="font-family:Arial,sans-serif">Another option is to engage directly with the manufacturers and ask them to commission the work. Please see the relevant blog</span><a href="http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/" class="" style="color:purple; text-decoration:underline"><span class="" style="font-family:Arial,sans-serif; color:rgb(17,85,204)">http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/</span></a><span class="" style="font-family:Arial,sans-serif"><span class="Apple-converted-space"> </span>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.</span></div>
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<span class="" style="font-family:Arial,sans-serif">Hope this helps.</span></div>
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<span class="" style="font-family:Arial,sans-serif">Thank you once more.</span></div>
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<span class="" style="font-family:Arial,sans-serif">All the best</span></div>
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<span class="" style="font-family:Arial,sans-serif">Petr</span></div>
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<span class="" style="font-family:Arial,sans-serif">OME Team</span></div>
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Dear Jean-Marie and Petr,<span class="apple-converted-space"> </span></div>
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Glad to hear you all are safely back, stay warm!</div>
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Thanks for asking about the czi structure for multi-block acquisition on Zeiss.</div>
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I found a smaller test set and zipped it up for sharing (<a href="https://www.dropbox.com/s/3wjxqd2i66zau2s/Archive.zip" class="" style="color:purple; text-decoration:underline"><span class="" style="color:purple">https://www.dropbox.com/s/3wjxqd2i66zau2s/Archive.zip</span></a> ,
approximately 57MB).</div>
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The structure of the output from zeiss is as below:</div>
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<span class="" style="font-size:8.5pt; font-family:Menlo; color:rgb(214,214,214)">├── PA01gfp_PF5mScarlet-1.czi</span></div>
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<span class="" style="font-size:8.5pt; font-family:Menlo; color:rgb(214,214,214)">│ ├── PA01gfp_PF5mScarlet-1.czmbi</span></div>
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<span class="" style="font-size:8.5pt; font-family:Menlo; color:rgb(214,214,214)">│ ├── PA01gfp_PF5mScarlet-1_AcquisitionBlock1.czi</span></div>
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<span class="" style="font-size:8.5pt; font-family:Menlo; color:rgb(214,214,214)">│ │ └── PA01gfp_PF5mScarlet-1_AcquisitionBlock1_pt1.czi</span></div>
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<span class="" style="font-size:8.5pt; font-family:Menlo; color:rgb(214,214,214)">│ └── PA01gfp_PF5mScarlet-1_AcquisitionBlock2.czi</span></div>
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<span class="" style="font-size:8.5pt; font-family:Menlo; color:rgb(214,214,214)">│ └── PA01gfp_PF5mScarlet-1_AcquisitionBlock2_pt2.czi</span></div>
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<span class="" style="font-size:8.5pt; font-family:Menlo; color:rgb(214,214,214)">└── zen\ blue.JPG</span></div>
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1. folder named with .czi</div>
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2. master file to open in zen blue is the .czmbi</div>
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3. each block has its own folder with .czi end</div>
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4. first block is 3 channel (3 x 2048 x 2048) for brightfield + red + green</div>
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5. second block is a timelapse of brightfield (7 x 2048 x 2048)</div>
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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).</div>
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<image001.jpg></div>
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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" class="" style="color:purple; text-decoration:underline"><span class="" 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).</div>
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Ghee Hwee</div>
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<span class="" style="font-family:Helvetica; font-style: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; font-size:10pt">The University of
Dundee is a registered Scottish Charity, No: SC015096</span></div>
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