Opening z-stack (czi) in Image J: invalid array

Hi all, I am trying to open a z-stack image (czi) that I took with our Axioscan Z1. The file is 285.2 MB. I know that I can use the Zen software to convert to a tiff, but when I do this, there is resolution loss that makes the image unusable for my purposes. I’ve attached an image of the error I get. Any help is appreciated.


How exactly are you opening your image in ImageJ/Fiji? Have you tried importing them via Bio-Formats? Also - there was an earlier thread on a similar topic that you might find helpful:

Fiji automatically has bio-formats uploaded, so yes I am using it. Also, I don’t want tiff files. I want to keep them as czi and work with them as czi.

Perhaps it’s best to bring in the @OMETeam & @dgault here … There have been issues with czi files previously:

Hi @nkmurra2 , are you using the Stitch Tiles option in the Bio-Formats Importer Options?

Also if you change the CZI autostitch option as below does that have any impact?
Plugins -> Bio-Formats -> Bio-Formats Plugins Configuration -> Formats -> Zeiss CZI -> Autostitch

If the above option is no use would you be able to upload the file to for testing

1 Like