CZI slide scanner image - BIO-formats

Dear @sebi06, Dear Bio-formats,

We’re encountering some weird behaviour of some czi slide scanner images. They were acquired on the same system but the Fiji’s plugin has some trouble opening some of them!

Please follow this link to the dataset with the czi files (and the corresponding ome.tiff exported from ZEN, which is working fine)

For a working czi we get

and the image looks like :

while for a not working czi we get :

with the image

Ideally, we’d prefer to store only the czi file (and thus not exporting the ome.tiff from Zen)

Thank you for your help/suggestions,



@oburri , @NicoKiaru , @stoffelc


Hi @romainGuiet

Hmmmmm… Did you use different compressions?

What is the difference from the acquisition side?