views as "group" in .czi and the autoloader

[schmiedc]

Hi David and Stephan,

a user brought me a Zeiss Lightsheet Z.1 multiview dataset were each view is contained in a different group. The rational is to make a lightsheet alignment for each view. Which is not possible when using only one group in Zen Black.

This is deviating from what I usually do in multiview datasets, thus I wondered if the autoloader can handle it. There is an option to assign the groups to Angles instead of tiles. So I guess it is in principle possible to process that or you guys thought about it and would like to make it available:

But when I want to define the .xml I get errors:

Would it be possible to make that a working feature?

Cheers, Christopher

[hoerldavid]

Hi @schmiedc, I just realized I never replied to this issue, sorry. Grouped .czis are something we want to support and I actually wrote a preliminary implementation https://github.com/PreibischLab/multiview-reconstruction/commit/fc104893d83983260505cf461865005e2f1ad60a in multiview-registration (on branch grouped-czi-fixes - that hasn't made it to the master branch yet for lack of testing). If you have a small-ish dataset lying around and can make it available to me, I would be happy to test my code on it.

[schmiedc]

Hi David,

thank you for supporting this. I try to get a hold of a smaller dataset from a user. But I think christmas holidays are getting in the way at the moment. I will get back to you once I have something.

Thank you! Christopher

[hoerldavid]

Hi Christopher,

the fix should be merged into master by now and it seems to work fine with our test datasets, so I'll close this. Should you run into any problem, let us know!

Thanks for the input, David