docs(tutorial): restore the napari screenshot cells and result images - #53
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xuefei-wang wants to merge 1 commit into
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docs(tutorial): restore the napari screenshot cells and result images#53xuefei-wang wants to merge 1 commit into
xuefei-wang wants to merge 1 commit into
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The v0.1.0 monorepo merge replaced both napari screenshot cells and the two embedded result images with the prose "Static documentation builds do not execute or embed GUI screenshots." The tutorial's two visual payoffs -- the multiplexed image with the CellSAM segmentation overlaid, and the per-cell-type label layers -- therefore vanished from the rendered page, leaving the "Visualizing results" sections with no output at all. The premise was wrong: napari renders headlessly under Xvfb + llvmpipe, which is how the currently-deployed site was built -- it still serves both _static/_generated/*.png. Restore the two `hide-cell` screenshot cells and the <img> embeds so the repo source matches the build that actually works. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01Qvo32Wvq8EHyA9jmFCXuXi
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Problem
A user reports that the tutorial "stripped out the important steps to run/visualize the results," comparing against
616d4b5.They're right. The v0.1.0 monorepo merge (
4a2d7ba) replaced both napari screenshot cells and both embedded result images with prose:So the tutorial's two visual payoffs — the multiplexed image with the CellSAM segmentation overlaid, and the per-cell-type label layers — disappeared from the rendered page. Both "Visualizing results" sections now end with no output at all.
Why the premise was wrong
napari does render headlessly (Xvfb + llvmpipe), and that is how the currently-deployed site was built. https://vanvalenlab.github.io/deepcell-types/site/tutorial.html still serves both images today:
_static/_generated/napari_img_and_segmentation.png_static/_generated/napari_celltype_layers.pngThe repo source and the published build had silently diverged. This restores the source to match the build that actually works.
Change
Restores the two
hide-cellnim.screenshot(...)cells and the two<img>embeds. Docs-only; no code touched.Verification
jupytextparses the tutorial: 45 cells / 24 code cells, 2 screenshot cells, 2 image embedspytest: 470 passed, 1 skippeddocs/site/tutorial.mdis byte-identical to the version that produced the live site, apart from one unrelated abstention-wording sentence left untouchedNot addressed here
The same report also says the model won't run. Everything testable offline is healthy —
pip install git+...@masterresolves (incl.deepcell_authfrom git), the deepcell-auth manifest maps2026-06-15tomodels/deepcell-types_2026-06-15_resmlp.pt/b819a7e0…, andpredict()runs fine against that checkpoint on this branch. The one link that can't be checked without a token is whether the bucket actually serves an asset with that hash. Tracking separately.Separately: gh-pages was last built 2026-07-12, which predates the deepcell-auth migration (#47, 2026-07-30) — the published site should be rebuilt from master once this lands.