[ome-users] multi-scene .czi files

[Sebastien Besson (Staff)]

Hi Oliver,

the Zeiss scene dimension should be supported by Bio-Formats and we certainly have
several representative CZI datasets including multiple scenes tested daily.

Could you first of all confirm you are using Bio-Formats 5.1.10 in Fiji? Also, can you give us
more detail about the issue: is an error thrown by Bio-Formats when opening the file or is a
single position opened with wrong dimensions? Finally do you have a sample file that you could
upload to http://qa.openmicroscopy.org.uk/qa/upload/ to reproduce the issue?

Best,
Sebastien

On 2 Jun 2016, at 10:25, Oliver Brookes <o.brookes at qmul.ac.uk<mailto:o.brookes at qmul.ac.uk>> wrote:


Hello, I've found that it's not possible to open multiple scene Zeiss images using bioformats in FIJI. Using the "positions" option on our Zeiss Elyra, it's possible to store multiple locations and automatically take pictures (very good for timelapse video). The positional info is stored in the .czi format as a "scene" dimension - the dimensions of the file are listed as XYCZTSB. I can open czi images, stacks and movies that are taken at single positions (anything where the dimensions of the .czi file are XYCZT). Is the extended .czi format not supported?


Thanks,


Oliver

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