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Multi-scene CZI files

Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats
Please note:
Historical discussions about the Bio-Formats library. Please look for and ask new questions at https://forum.image.sc/tags/bio-formats

If you are having trouble with image files, there is information about reporting bugs in the Bio-Formats documentation. Please send us the data and let us know what version of Bio-Formats you are using. For issues with your code, please provide a link to a public repository, ideally GitHub.

Re: Multi-scene CZI files

Postby MSomerville » Wed Oct 10, 2018 2:02 pm

Hi there,

Sorry for the delay I was having issues uploading the files but that's now complete.

Best wishes,

Michelle
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Re: Multi-scene CZI files

Postby dgault » Thu Oct 11, 2018 11:26 am

Thank you, I have been able to test the submitted files this morning and was able to reproduce the behaviour you were seeing. The good news is that there is an easy work around for it. If you are using FIJI you can set the CZI autostich option and this should enable the files to be read and opened.

You can set the option using:
Plugins > Bio-Formats > Bio-formats Plugins Configuration > Formats > Zeiss CZI > Autostich

However the original issue with autostich turned off does look like a bug and I have opened a Trello card on the Bio-Formats board for that issue https://trello.com/c/BiD7ToLT/287-czi-f ... itched-off
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dgault
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Re: Multi-scene CZI files

Postby MSomerville » Fri Oct 12, 2018 10:04 am

Thank you very much for looking into this for us, it's much appreciated. I will try opening the files with your suggestion.

Best wishes,

Michelle
MSomerville
 
Posts: 4
Joined: Mon Oct 08, 2018 1:38 pm

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