ImportError: numpy.core.multiarray failed to import` / `AttributeError: _ARRAY_API not found` when importing stardist

[pchegom]

Hi, I'm running into persistent import errors when trying to use stardist in a Colab environment. Even after reinstalling dependencies carefully, I still encounter the following:

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Error Tracebacks:

ImportError: numpy.core.multiarray failed to import
AttributeError: _ARRAY_API not found
ModuleNotFoundError: No module named 'stardist'

These occur especially when importing from:

from stardist.utils import fill_label_holes, random_label_cmap, calculate_extents, gputools_available

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What I've Tried:

1. Uninstalled and reinstalled packages with pinned versions:

   pip uninstall -y stardist csbdeep gputools
   pip install numpy==1.23.5
   pip install csbdeep==0.7.2
   pip install --no-build-isolation --no-cache-dir stardist==0.8.3

2. Restarted the Colab runtime.

3. Attempted with and without TensorFlow (tensorflow==2.15).

4. Tried forcing reinstall of numpy with different versions (1.24.x, 1.23.5, 1.26.x, etc.)

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Observation:

I suspect the issue is due to conflicting NumPy version requirements between stardist and other dependencies (e.g. csbdeep, scikit-image, etc.). Some packages internally install a newer version of numpy, causing stardist to break at import due to binary incompatibility (e.g., missing _ARRAY_API or failure in multiarray).

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Environment:

• Platform: Google Colab
• Python: 3.11.8
• numpy: 1.23.5 (tried other versions too)
• csbdeep: 0.7.2
• stardist: 0.8.3

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Request:

Is there a known compatible set of versions for stardist, csbdeep, and numpy for Python 3.11? Alternatively, should I downgrade to an older Python version (e.g. 3.9) to avoid these conflicts? Any guidance or environment YAML would be very helpful.

Thanks in advance for your support!

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[pengyuyahn]

May I ask if you have solved this problem? I also encountered a similar issue