Look-up-table/Jupyter Notebook Segmentation Image import and visualization error

[DarthRevan109]

Description

Unable to view and thus segment images in look-up-table demos in allen-classic segmentation via jupyter notebook. Follow error message is received when running the jupyter notebook:

After running the "Loading the data" commands (this happens with both 2D and 3D data sets, single channel images):
Failed to parse XML for the provided file. Error: not well-formed (invalid token): line 1, column 6
(1, 1, 20, 1024, 1024)

When I continue the pipeline, I get the following error in the "Preview of the image" commands:

np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

IndexError Traceback (most recent call last)
~\AppData\Local\Temp\ipykernel_31488\3651088532.py in
5 if N_CHANNELS==1:
6 ax.axis('off')
----> 7 ax.imshow(IMG[0,0,0,MID_SLICE,:,:], cmap=plt.cm.gray)
8 else:
9 for channel in range(N_CHANNELS):

IndexError: too many indices for array: array is 5-dimensional, but 6 were indexed

Expected Behavior

Images should be able to be visualize then segmented (previously worked for me, roughly 1 year ago)

Reproduction

1. Run jupyter notebook from anaconda (in aics-segmentation environment)
2. Pick any playground (dots for example)
3. run all steps until getting to "Loading the data"
4. Receive error

Environment

Jupyter notebook via anaconda

[antoineruzette]

Dear,

I get the same error. Were you able to fix it?

And it logically follows that the view test was not successful with this error arising:

Model class 'ViewerModel' from module 'itkwidgets' is loaded but can not be instantiated
TypeError: o._deserialize_state is not a function

Thank you!