Zeiss CZI file from colour cameras in OMERO v5.1

[mattc]

We are having a couple of issues with Zeiss CZI files from colour cameras. First of all although BioFormats successfully opens a single channel image from a colour camera but it fails to open multi channel files. When it does open a single channel file it splits the RGB into 3 channels and makes them grey. It might be useful to note that Zen Black also struggles with multi channel images (also splits the RGB) but Zen Blue does it successfully.

[mlinkert]

Could you please let us know which version of Bio-Formats you're using, and in which application (e.g. ImageJ, MATLAB, ...)? This is not necessarily unexpected behavior, but our recommendations for how to turn the separated channels into a single RGB image will depend on how you're using Bio-Formats.

[mattc]

Hi,

We're using v5.12 of the OMERO server and clients and i'm viewing the image in ImageJ. I've uploaded a sample czi file (zeiss_czi_qa.czi) to qa.

Thanks for your help,

Matt.

[bramalingam]

Hi,

Thank you for submitting your files to our QA server.

Testing this locally with the latest version of Bio-Formats (5.1.6) and OMERO(5.1.4 and 5.2.0), we were unable to reproduce the bug. I am listing my testing results here for the zeiss_czi_qa.czi image,
1) The image opens in grey scale mode, in Zen Blue Lite,Bio-Formats, and OMERO as well.
2) It was identified as a single channel image in all cases(Zen Blue Lite, Bio-Formats and OMERO)

So a simple upgrade to the latest version of OMERO(5.1.4 or 5.2.0) should solve your issue.
Since this file confirms with the single-channel issue you were discussing, could you also upload the multi-channel image. This would help us troublshoot the multi-channel issue, in better detail.

Please keep us posted if the upgrade does not solve your issue.

Best,
Balaji