Issue concerning .oif files, "Invalid Z index error."

Hi again!

Another problem I’d like to report.
When I try to input z-stack data from a folder, I get this error message:
"Error while processing LoadImages:
Invalid Z index: 1/1"
Also it tries to load ~400 pictures, though there are only 13 tif files in the directory.

Our default folder structure looks like this:
2012-12-12_1-35h_5um Calc0018.oif.files
2012-12-12_1-35h_5um Calc0018.oif

When I delete the 2012-12-12_1-35h_5um Calc0018.oif file, which is outside the input folder specified in LoadImages, everything works fine.

I guess it’s related to the admittedly quite uncommon naming conventions of our microscopes software (folder names with dots, doh).


Hi Christoph,

Would you mind posting your pipeline plus an example .oif file? I wouldn’t expect that the folder nomenclature would make a difference, but I’d like to try replicating the error with some example files.


Here’s one minimal example:
The error is in the loadImages module, so I removed the rest of my pipeline. I included a small folder with example files.

I also totally forgot to mention that I work on windows here. I could imagine it’s an OS-specific problem.

Christoph (569 KB)

Just replicated the error on Mac OS.

(Sorry for the long delay in responding to this post.)

In LoadImages, rather than using “tif,tiff,flex,zvi movies” as the file type, try just using the “individual images”. Unless I’m misunderstanding something about the TIF files themselves, making this change seems to get things working.