Unable to access to all series in .czi files

[ShanJiangEmugen]

Hi there,

I currently have some images taken from Zeiss AxioScan, which stored images in a slightly different .czi format than my previous scanning. The new .czi file will stack all slices/scenes together and name each of them as "series #" when I open it in ImageJ, please see the attached ImageJ screenshot. However, when I load those .czi files with Python, I cannot select the "series #". It only loads the first "series". Are there any features in this bioio that can handle this issue? I have tried AICSImageIO, but seems it has nothing to do with this issue.

I used Google Colab for this project, so there shouldn't be any environment-related issues.

Thanks a lot in advance!

[toloudis]

It sounds like what you want is the concept of BioImage.scenes and BioImage.set_scene:
https://bioio-devs.github.io/bioio/bioio.html#bioio.bio_image.BioImage.scenes

[ShanJiangEmugen]

Thanks for your help!

I tried the BioImage.scenes method but it still didn't recognize the "Series". Please see the attached.

I guess that's one of the new features of Zessi equipment. My current workaround is to get each image through ImageJ Marco.

[BrianWhitneyAI]

hey @ShanJiangEmugen Thanks again for your submission. I'm sorry the .scenes functionality isn't working for you. Do you have some test files that you could provide so I can look into this issue further?