Large CZI file fails silently (?)

[Omnistic]

System and Software

• aicspylibczi Version: 3.3.1
• Python Version: 3.13.5
• Operating System: Windows 11 Pro

Description

I am imaging the content of a 96-well plate.

In every well, there are 4 tiles (2x2).

I made a first image of only 2 wells for prototyping. My code works fine.

Then, I made a second image of 60 wells (inner wells).

The same code runs, but it silently fails when reading the mosaic. What I mean by that is that it doesn't throw an error, and the rest of the code is simply ignored.

If I use a scale factor of 0.5, my code works again.

The 2-wells image is 220MB and the 60-wells image is 6.5GB. My RAM is 32GB and doesn't get filled during the execution of the code (only fills up to 27GB).

Expected Behavior

I was expecting an error to be thrown. I had the expectation that this was going to be challenging, but at the same time, I was confident that 6.5GB was well below my 32GB internal memory, which is why I didn't suspect this to be the problem in the beginning.

Reproduction

With the following snippet:

overview = CziFile('overview_2_tiles.czi')
test_img = overview.read_mosaic(C=0)
print(test_img.shape)

overview = CziFile('overview_60_tiles.czi')
test_img = overview.read_mosaic(C=0)
print(test_img.shape)

I get the following output:

(1, 5720, 20827)

The code completes without throwing any error.

Environment

I use PIXI and I have the following dependencies:

[dependencies]
numpy = ">=2.3.2,<3"
aicspylibczi = ">=3.3.1,<4"
pandas = ">=2.3.1,<3"
napari = ">=0.5.0,<0.6"
pyqt = ">=5.15.11,<6"