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Add normalization and contrast tutorial#9

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timtreis wants to merge 2 commits into
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feat/normalization-tutorial
Open

Add normalization and contrast tutorial#9
timtreis wants to merge 2 commits into
mainfrom
feat/normalization-tutorial

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Summary

Adds a tutorials/normalization_and_contrast.ipynb tutorial covering the norm= argument end-to-end on the blobs dataset:

  • what a norm is and when limits autoscale
  • fixed contrast limits Normalize(vmin, vmax)
  • clipping: under/over colors vs clamp
  • LogNorm, PowerNorm, SymLogNorm
  • percentile contrast via PercentileNormalize (broadcast + per-channel list)
  • combining with transfunc, true RGB images
  • norms on shapes / points / labels, and the datashader caveat
  • the edge cases the renderer validates

Committed with outputs; linked into tutorials/index.md with a thumbnail in _static/img/normalization_and_contrast.png.

⚠️ Depends on a release

The notebook uses PercentileNormalize (scverse/spatialdata-plot#725), which is on main but not yet in a published release. The execute CI re-runs against the latest spatialdata-plot release, so it will fail until a release including #725 is published. Outputs in the committed notebook were generated against the dev build.

Companion gallery PR in scverse/spatialdata-plot links this tutorial with the same thumbnail.

Covers the norm= argument end-to-end on the blobs dataset: fixed contrast
limits, clip under/over vs clamp, LogNorm/PowerNorm/SymLogNorm, percentile
contrast via PercentileNormalize, per-channel norm lists for images, and
norms on shapes/points/labels. Linked into tutorials/index.md.

Note: PercentileNormalize ships in the next spatialdata-plot release; the
execute CI will pass once that release is published.
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📖 Docs preview: https://scverse.org/spatialdata-plot-notebooks/pr-9/gallery.html

Built from 3ce8dbf; redeployed on every push.

github-actions Bot pushed a commit that referenced this pull request Jun 20, 2026
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