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Refactor Xenium + Visium paths and use better names

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#39 1 comment 0 reactions 0 assignees View on GitHub

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Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
45/100
Issue type
Refactor
Clarity
Clearly specified
Activity status
Stale
Tech stack
jupyter-notebook, python
Domain
documentation

Research direction

Start with the paths in 00_xenium_and_visium.ipynb, 01_xenium_and_visium.ipynb, and 02_xenium_and_visium.ipynb, then review how config.py should hold them. Update the notebooks to use manual_annotations.zarr instead of sandbox.zarr and verify that all paths are centralized and the renamed S3 copy is referenced.

Written by the indexing model from the issue text.

Description

  • all the paths used in notebooks 00_xenium_and_visium.ipynb, 01_xenium_and_visium.ipynb and 02_xenium_and_visium.ipynb should be placed in a config.py file
  • sandbox.zarr was a poorly chosen name, rename it to manual_annotations.zarr. I have already made a copy in the S3 bucket of that file (so that now both sandbox.zarr.zip and manual_annotations.zarr.zip are present), so one needs just to adjust the notebooks.
Dominant language
Jupyter Notebook
Stars
67
Forks
26
Avg merge
4m
Merged PRs (30d)
1

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