our Zeiss Lightsheet Z1 has been upgraded to the new Zeiss Lightsheet 7, and with it came some changes in the Zen software. One such change addressed how the Zen software handles a tiled acquisition, which also leads to a change in the metadata of the czi that concerns the tiles, and hence Bio-Formats (tested v.6.6.0) does not recognize the tiles as individual series anymore.
As a consequence, our downstream processing (BigStitcher) that relies on Bio-Formats fails.
I have uploaded a small (~1.8 GB) .czi dataset (ID 165676) to your web server here:
and for temporary direct download here (valid until 2021-03-17):
It contains: 4 tiles, 16 z, 2 channels, 2 illuminations, 1 time point and 1 angle.
I also contacted Zeiss and have asked for more information about where exactly the tile info and stage coordinates can now be found in the czi, but its also likely that I might not fully understand the details.
However, let me know in case there are specific questions that you have, and I’ll be happy to relay them to Zeiss in case you don’t have a direct contact.
On that note, tagging in @sebi06 from Zeiss, in case there is something that he can chip in on (thanks Sebi!)
Thank you for your help!