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bioio-devs / bioio-czi

A BioIO reader plugin for reading CZI files.
GNU General Public License v3.0
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Unable to access to all series in .czi files #20

Open ShanJiangEmugen opened 1 month ago

ShanJiangEmugen commented 1 month ago

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!

截图 2024-10-31 14-57-25

toloudis commented 3 weeks ago

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 commented 3 weeks ago

Thanks for your help!

I tried theBioImage.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.

image