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Reading czi file #4

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DeepaMahm opened this issue Jul 1, 2020 · 0 comments
Closed

Reading czi file #4

DeepaMahm opened this issue Jul 1, 2020 · 0 comments

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@DeepaMahm
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DeepaMahm commented Jul 1, 2020 •
edited

Hi @bnsreenu

Firstly, thank you very much for the amazing videos.
I am sorry, this is not really an issue.

I've a few doubts in reading czi file and I would like to ask those here. Following the video tutorial, the czi file is imported in python like this

import czifile
from skimage import io

img = czifile.imread('file.czi')
print(img.shape)

The output is
(1, 1, 3, 1, 48, 1024, 1024, 1)
I couldn't completely understand what each value in the output refers to

Does 3 denote the number of channels?
Does 48 denote the number of slices in the z-stack for each channel?

I would like to save the z-stack corresponding to channel 1 in tiff format. Could you please offer some advice on how this can be done?
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@DeepaMahm