User notebook showcasing SpatialData speed
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- Dominant language
- Python
- Stars
- 394
- Forks
- 95
- Avg merge
- 4d 3h
- Merged PRs (30d)
- 7
Description
Is your feature request related to a problem? Please describe.
Right now there is no clear showcase of the performance and speed of the SpatialData library, while this is one of it's big benefits.
Describe the solution you'd like
Create a notebook opening a large dataset, plotting the overview, querying a subset, aggregating signal and plotting results as quickly. Show the time with a counter and %%timeit per cel.
Describe alternatives you've considered
There is no clear plot of this in the paper. It's similar also to the plotting performance notebook, but more general.
Additional context
Add any other context or screenshots about the feature request here.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing the existing plotting performance notebook mentioned in the issue and identify a suitable large SpatialData dataset. Build a notebook that opens the dataset, plots an overview, queries a subset, aggregates signal, and plots the results, including a counter and %%timeit for each step; done means the performance showcase is reproducible and covers all requested operations.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- data-visualization, documentation, performance
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100