Open Microscopy Environment

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.

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.

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.

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