Colab inference demo incompatible with current MONAI and NumPy

Hi there,

I was trying out the Colab inference notebook ([here])(https://colab.research.google.com/github/MMathisLab/CellSeg3d/blob/main/Notebooks/Colab_inference_demo.ipynb#scrollTo=IFbmZ3_zAm-1) and I've gotten the following error. All original code above this line ran without error:

result = cs3d.inference_on_images(
    demo_image,
    config=inference_config,
)

WARNING:napari_cellseg3d.utils:Caught TypeError: SwinUNETR.__init__() got multiple values for argument 'in_channels'
ERROR:napari_cellseg3d.utils:SwinUNETR.__init__() got multiple values for argument 'in_channels'
Traceback (most recent call last):
  File "/usr/local/lib/python3.12/dist-packages/napari_cellseg3d/code_models/models/model_SwinUNetR.py", line 34, in __init__
    super().__init__(
TypeError: SwinUNETR.__init__() got multiple values for argument 'in_channels'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.12/dist-packages/napari_cellseg3d/code_models/worker_inference.py", line 859, in inference
    model = model_class(
            ^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/dist-packages/napari_cellseg3d/code_models/models/model_SwinUNetR.py", line 47, in __init__
    super().__init__(
TypeError: SwinUNETR.__init__() got multiple values for argument 'in_channels'
--------------------
Parameters summary :
Model is : SwinUNetR
Window inference is enabled
Window size is 64
Window overlap is 0.25
Dataset loaded on cuda device
--------------------
MODEL DIMS : [64, 64, 64]
Model name : SwinUNetR
Instantiating model...

Changing numpy and monai versions solved the issue for me:

!pip install -U "numpy>=2.1,<2.6" "monai==1.3.2"

import numpy, monai
print("NumPy:", numpy.__version__)
print("MONAI:", monai.__version__)

NumPy: 2.4.6
MONAI: 1.3.2

Then updating reshape to shape to match different numpy version:

from pathlib import Path

p = Path("/usr/local/lib/python3.12/dist-packages/napari_cellseg3d/code_models/worker_inference.py")
s = p.read_text()
s = s.replace("np.reshape(volume, newshape=(1, *volume.shape))",
              "np.reshape(volume, (1, *volume.shape))")
p.write_text(s)

print("Patched:", p)

@msayr

Hello @msayr,

Thanks a lot for reporting; I’m currently updating the package to run properly on Python 3.12 and to fix several deprecated/old calls, including the newshape issue.

The SwinUNETR.__init__() got multiple values for argument 'in_channels' error looks related to MONAI API/version compatibility, so I’m checking that as part of the update as well. In my limited local testing, the plugin is now running reasonably well with recent napari/MONAI versions, but I remember this being broken by a MONAI update, they might have fixed it in a subsequent release however as I got it to run locally. Will investigate this further.

Thanks again!

Best,
Cyril

Closed automatically by #120, re-opening until released/fix is confirmed

@msayr

Hello @msayr,

Version 0.2.4 is now live, which moves the supported Python versions to 3.10-3.12.

This fixes all deprecation errors, and I've confirmed that all models run properly locally.
Please let me know if it still fails on Colab with the latest!

Thanks again,
Cyril

@C-Achard

Hi @C-Achard thank you very much for the prompt response! I just tested the notebook and it looks like pyclesperanto is required but now missing:

# @title Load libraries
import napari_cellseg3d
from tifffile import imread
from pathlib import Path
from napari_cellseg3d.dev_scripts import remote_inference as cs3d
from napari_cellseg3d.utils import LOGGER as logger

import logging

logger.setLevel(logging.INFO)

output:

_/usr/local/lib/python3.12/dist-packages/pyclesperanto/__init__.py:29: RuntimeWarning: No pyclesperanto backend installed.
Install one with:
  pip install pyclesperanto[opencl]   # for OpenCL
  pip install pyclesperanto[cuda]     # for CUDA
  pip install pyclesperanto[metal]    # for Metal
  pip install pyclesperanto[all]      # for both
  warnings.warn(_

###########

demo_image_path = "/content/CellSeg3D/examples/c5image.tif"
demo_image = imread(demo_image_path)
inference_config = cs3d.CONFIG
post_process_config = cs3d.PostProcessConfig()
# select cle device for colab
import pyclesperanto_prototype as cle
cle.select_device("cupy")

output:

---------------------------------------------------------------------------
ModuleNotFoundError                       Traceback (most recent call last)
[/tmp/ipykernel_5093/3519197974.py](https://localhost:8080/#) in <cell line: 0>()
      4 post_process_config = cs3d.PostProcessConfig()
      5 # select cle device for colab
----> 6 import pyclesperanto_prototype as cle
      7 cle.select_device("cupy")

ModuleNotFoundError: No module named 'pyclesperanto_prototype'

---------------------------------------------------------------------------
NOTE: If your import is failing due to a missing package, you can
manually install dependencies using either !pip or !apt.

To view examples of installing some common dependencies, click the
"Open Examples" button below.
---------------------------------------------------------------------------

@msayr

Hi @msayr,

Yes, apologies, we are no longer using the prototype version, this should work by removing the _prototype suffix.

There was a small issue with the release that required immediate attention, I will check the Colab notebook more thoroughly soon.

Best,
Cyril

Okay, the issue was a bit sneakier: the Open in Colab URL was pointing to the MMathisLab fork instead of this repo, so it was not showing the latest version.

I will PR a new version with uv, check it works fine, and get back to you!

@msayr

@msayr Here is the link to the updated notebook:
https://colab.research.google.com/github/AdaptiveMotorControlLab/CellSeg3D/blob/main/notebooks/Colab_inference_demo.ipynb

Let me know if there are any issues! Thanks again.

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Colab inference demo incompatible with current MONAI and NumPy #119

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Colab inference demo incompatible with current MONAI and NumPy #119

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C-Achard commented on May 19, 2026

C-Achard commented on May 19, 2026

C-Achard commented on May 21, 2026

msayr commented on May 21, 2026

C-Achard commented on May 21, 2026

C-Achard commented on May 21, 2026

C-Achard commented on May 22, 2026

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