AllenInstitute / openscope_databook

OpenScope databook: a collaborative, versioned, data-centric collection of foundational analyses for reproducible systems neuroscience 🐁🧠🔬🖥️📈
https://alleninstitute.github.io/openscope_databook
Other
63 stars 19 forks source link

Visualize neuropixel probes fails on Google colab #247

Closed rcpeene closed 1 year ago

rcpeene commented 1 year ago

the notebook visualize_neuropixel_probes.ipynb yields the following error in the final render cell:

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
[<ipython-input-8-09213273d023>](https://localhost:8080/#) in <cell line: 1>()
----> 1 ccf = CCFWidget(markers=[points])

3 frames
[/usr/local/lib/python3.10/dist-packages/itkwidgets/widget_viewer.py](https://localhost:8080/#) in _update_rendered_image(self)
    518 
    519             if self.image:
--> 520                 self.shrinker.UpdateLargestPossibleRegion()
    521             if self.label_image:
    522                 self.label_image_shrinker.UpdateLargestPossibleRegion()

RuntimeError: /work/ITK-source/ITK/Modules/Core/Common/src/itkDataObject.cxx:367:
Requested region is (at least partially) outside the largest possible region.
rcpeene commented 1 year ago

Also looks to be failing our tests?

rcpeene commented 1 year ago

After fixing the environment issue with zarr, the notebook still fails. This is a problem with CCFwidgets. I filed an issue, unlikely it will be addressed any time soon.

jeromelecoq commented 1 year ago

@rcpeene to edit the notebook to mention the issue with Colab and explain which platform it works with.