CZI files with parentheses in name

This is perhaps a BioFormats issue and not a Fiji issue. Regardless, maybe someone can help.

Take two CZI files, name them:

image.czi
image (B).czi

Drag the second one into Fiji and the first file opens. It feels like something to do with the way CZI series are handled as if only the second file is present, it opens just fine. All options are unchecked in the CZI section of bioformats and the only box checked in the BioFormats importer window is Autoscale.

If you want to try it, some examples files are here:
czi_files.zip (4.8 MB)

Does anyone have an idea how to prevent this behaviour in Fiji?

4 Likes

Hi @dnmason,

sorry for the delay. This thread escaped our radar. The CZI reader indeeds includes some logic to try to detect and group multi-file CZI datasets as this variant of the file format had been brought to our attention. For those interested in the code, the grouping logic happens here and here).

In your case, we might need to refine this logic so that a file called test (B).czi is never considered for grouping. In the meantime, I would expect selecting Open Files Individually in the importer window should suffice to only open the file dragged to the window.

Best,
Sebastien

Can we use the samples linked in CZI files with parentheses in name? Can these be made public?

3 Likes

hi @s.besson thanks for the reply.

This does indeed work for opening the correct file.

You’re welcome to use the files linked without restriction for any purpose you like.