Error opening .czi files in Fiji

Hello All!

I’m pretty new to Fiji/ImageJ, but I couldn’t find this issue in any user guide. When I try to open certain .czi files, I get a pretty confusing error message. These files are images I took with a Zeiss Axio Imager Z2 confocal microscope, that I transferred to my computer via pen drive. Using Fiji, I’m able to successfully open half of the files I transferred. The other half, which are mixed in with the good files, give me variations of this message when I attempt to open them.

I have tried re-downloading the files several times on different pen drives, with no success. It seems that most of the files I can open are Z-stacks, if that makes any difference. I also just got Fiji earlier this week, so I don’t think it’s a matter of needing to update the software, although I am willing to try that.

Thanks for reading,


It would help if you could host the files somewhere that someone with FIJI experience could take a look at them. That said, are you dragging and dropping the files in? It might be a variant of:
In which case you might want to try the BioFormats importer function.

Thanks for the suggestion! I wasn’t aware of the Bioformats function. I just tried that and it said that the files were corrupted, so I probably made a mistake when I saved the file for the very first time.