Aicssegmentation not found in Jupyter, Classic Segmentation

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1

Hi,

I am new to python and jupyter. I have been getting this error in demo_TNNI1 on jupyter notebook:

ModuleNotFoundError Traceback (most recent call last)
~\AppData\Local\Temp\ipykernel_8960\399458622.py in
3 # package for 3d visualization
4 from itkwidgets import view
----> 5 from aicssegmentation.core.visual import seg_fluo_side_by_side, single_fluorescent_view, segmentation_quick_view
6 import matplotlib.pyplot as plt
7 plt.rcParams[“figure.figsize”] = [12, 8]

ModuleNotFoundError: No module named ‘aicssegmentation’

I do have a file called visual.py in a folder called “core” in a folder called “aicssegmentation”. However, jupyter isn’t seeing that for some reason.

When setting up the segmenter, I had to download everything as a zip file because the command “pip install -e .[all]” did not work for me. It is in my folder “aics-segmentation”.

If anybody can help me, it would be greatly appreciated.

2

Hi @jcvance ! I think this is likely a result of not being to pip install in editable mode. What are the errors you’re running into with pip install -e .?

3

Hi!

I was able to get help in person before this came through. I was getting this message:

ERROR: file:///C:/aics-segmentation does not appear to be a Python project: neither ‘setup.py’ nor ‘pyproject.toml’ found.

I was able to get around this by setting my directory to the folder that held the required files. Once I successfully installed that, aicssegmentation did work!

Thank you for your response!

4

Glad to hear it! Feel free to reach out if more questions come up.