Add notebook illustration cp-measure based featurisation#143
Open
timtreis wants to merge 5 commits into
Open
Conversation
|
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
…a API Rebuild tutorial_cpmeasure against sq.experimental.im.calculate_image_features (SpatialData-native, per-object). Two parts: single-cell profiling on the Xenium cells() dataset, and region profiling on Visium H&E spots. Drops the pre-merge sketch (sq.exp, measurements=, cpmeasure:* flags, local zarr) and the committed outputs; outputs are regenerated against the released squidpy. Add tutorial_cpmeasure to the tutorials index.
Run end-to-end against the dev build and commit rendered outputs (5 figures). Fixes found during execution: - pass scale='scale0' to the morphology-only call (cell_labels is multiscale) - drop non-finite feature columns before AND after scaling (float32 variance underflow on near-constant columns nulls a column, breaking PCA) - %matplotlib inline + warnings suppression for a clean rendered gallery Outputs are from the dev build; they will be regenerated against the released squidpy per the deploy plan.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
No description provided.