Open CZI file with multiple series

[Omnistic]

Hi everyone,

I am not familiar with aicsimageio and the CZI file format. However, when I open my CZI file in Fiji, I get asked which series I want to open (I have 240 series in this file). In aicsimageio, whether I use AICSImage or the CziReader, I only get the first series. This code:

from aicsimageio import AICSImage

img = AICSImage("my_file.czi")
print(img.dims)

with my data returns (I do indeed have two channels and three z-slices):
<Dimensions [T: 1, C: 2, Z: 3, Y: 1900, X: 1900]>
However, the same data when drag-and-dropped into Fiji prompts me to choose among the 240 series. Can somebody shine some light on what I am doing wrong? My CZI file is about 10GB, and a single series is about 43MB so this data exists in my CZI file. Thanks for the help.

Omni

[toloudis]

Hello! Thanks for the question.

1. If you can, switch to bioio. aicsimageio is currently in maintenance mode. Bioio is its successor. Same api, just a different organization of packages.
2. We use scene instead of series. By default you get the first scene. But the AICSImage (BioImage in bioio) has a scenes property which you can enumerate and a set_scene function you can call.

[Omnistic]

Perfect, thank you for the information about BioIO. There I could find the methods to work with scenes. I should probably start a new discussion there, but do you know if we can set_scene with multiple integers, such as a list? Say, I want to open scene 20 to 40 for example. Thanks a lot for your help and take care,

Omni

[toloudis]

It wouldn't make sense to call set_scene with a list. It sets the current scene on the BioImage so that all the other calls to get metadata and data use that context. The thing to do is to write a loop over your list of scenes and call set_scene on each one.

[Omnistic]

Thank you @toloudis. I guess it will make more sense when I get familiar with the file format.
Take care,

David