docs: add multichannel & fluorescence images tutorial - #17
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New tutorials/multichannel_images.ipynb using the real Xenium cells dataset (squidpy), whose morphology_focus image has four named fluorescence channels (DAPI, ATP1A1/CD45/E-Cadherin, 18S, AlphaSMA/Vimentin). Covers the render_images surface beyond a single channel: - channel= selection by name, and channel lists - the default multichannel composite - per-channel contrast with PercentileNormalize (fluorescence is heavy-tailed) - cmap vs palette: per-channel palette LUTs for additive compositing (and the white-overlay warning that motivates palette over cmap) - grayscale (3-channel desaturated view) and channels_as_legend Executed against spatialdata-plot v0.4.1; committed with outputs. Adds the gallery card + toctree entry and a thumbnail. Closes the P0.1 gap from the 0.4.0/0.4.1 doc-coverage analysis.
…le channel-order caveat, LUT acronym
…r integer-named axes)
Default composite gave every channel the same legend colour. Subset to three channels with an additive palette so the legend maps to what is drawn; note why white-based cmaps wash the composite out. Pin squidpy>=1.8.2 (first release with datasets.cells). Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011JMbY8asahxaytthjvCKDv
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…nail Place the legend in the empty lower-left corner, white and frameless so it reads on the black composite; the same view is now the gallery thumbnail. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011JMbY8asahxaytthjvCKDv
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011JMbY8asahxaytthjvCKDv
Uses frameon/labelcolor from spatialdata-plot#772; needs the next spatialdata-plot release. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011JMbY8asahxaytthjvCKDv
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_011JMbY8asahxaytthjvCKDv
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Summary
Adds
tutorials/multichannel_images.ipynb— therender_imagesstory beyond a single channel, the biggest documentation gap for fluorescence / multiplexed-imaging users (Xenium, CODEX, IMC, CyCIF).Uses the real Xenium
cellsdataset (squidpy.datasets.cells(), 2.8 MB, cached) — itsmorphology_focusimage has four named fluorescence channels (DAPI, ATP1A1/CD45/E-Cadherin, 18S, AlphaSMA/Vimentin).Covers:
channel=selection by name and by listPercentileNormalize(fluorescence is heavy-tailed) — pass a list of normscmapvspalette: per-channel palette LUTs for additive compositing, and the white-overlay warning that motivatespaletteovercmapgrayscale(3-channel desaturated view) andchannels_as_legendExecuted against spatialdata-plot v0.4.1, committed with outputs. Adds the gallery card + toctree + thumbnail.
First of the documentation-expansion series from the 0.4.0/0.4.1 gap analysis (P0.1). Cross-links the pending normalization tutorial (#9) for norms in depth.