Why can't I read my czi file? PixelType( Bgra32 ): numberOfSamples: Pixel Type unsupported by libCZI

[zerosky010]

System and Software

• aicspylibczi Version: 3.2.0
• Python Version:3.10
• Operating System: Windows

Description

A clear description of the bug
I'm just starting to learn about czi file handling.
However, when I am running a demo script ,

        filepath='sample.czi'
        import numpy as np
        from aicspylibczi import CziFile
        from pathlib import Path
        import matplotlib.pyplot as plt
        pth = Path('sample.czi')
        czi = CziFile(pth)

It turns out:

Traceback (most recent call last)
        Cell In[13], line 8
                  5 import matplotlib.pyplot as plt
                  7 pth = Path('sample.czi')
         ----> 8 czi = CziFile(pth)
                  10 # Get the shape of the data, the coordinate pairs are (start index, size)
                  11 dimensions = czi.get_dims_shape()  # [{'X': (0, 1900), 'Y': (0, 1300), 'Z': (0, 60), 'C': (0, 4), 'S': (0, 40), 'B': (0, 1)}]
        
        File e:\\anaconda3\\envs\apari-env\\lib\\site-packages\\aicspylibczi\\CziFile.py:63, in CziFile.__init__(self, czi_filename, verbose)
                  60 import _aicspylibczi
                  62 self.czilib = _aicspylibczi
          ---> 63 self.reader = self.czilib.Reader(self._bytes)
                  65 self.meta_root = None
        
        PylibCZI_PixelTypeException: PixelType( Bgra32 ): numberOfSamples: Pixel Type unsupported by libCZI."

How can I fix this problem? Or how to convert the format？

[heeler]

From the message I believe it's a lack of support in the libczi library that Zeiss released. I'll look at the code to double check later. If you're looking to gain familiarity with image reading I'd suggest looking at bioio and download a czi image from the test resources in the aicspylibczi repository.
Hope that helps.

[zerosky010]

Thank you for your suggestion! I’ll focus on learning bioio to get familiar with image reading. I really appreciate your help!