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docs: migrate to Zensical and overhaul the documentation - #157

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tlambert03 wants to merge 30 commits into

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docs-zensical

Open

docs: migrate to Zensical and overhaul the documentation#157
tlambert03 wants to merge 30 commits into
mainfrom
docs-zensical

Commits on Oct 11, 2026
- docs: migrate to Zensical and overhaul documentation
  
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- docs: interactive spectra chart (Observable Plot), JS photometry tested against microsim
  
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- docs: interactive photon budget and saturation charts
  
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- docs: interactive detector charts (SNR, EMCCD excess noise, PMT gain, HyD dead time)
  
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- docs: skill for checking the charts' JavaScript physics; contributing notes
  
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- docs: tutorials as notebooks, with Open in Colab and download buttons
  
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- docs: interactive noise and pinhole explorers
  
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- docs: update check-js-physics skill for the camera simulation
  
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- docs: review fixes (wording, tables, crosstalk example, chart tweaks)
  
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- docs: render math and charts inside link previews
  
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- docs: sample examples (MatsLines, COSEM, Allen neurons); prose-check skill
  
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- docs: crosstalk chart controls in two columns (fluorophores, then channels)
  
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- docs: generate the API reference with api-autonav
  
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- docs: hide internal modules from the API reference, group the overview by topic
  
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- Merge branch 'main' into docs-zensical
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- docs: exclude microsim.illum from the API reference, silence griffe warnings for pydantic models, use the canonical site URL
  
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- docs: raise the noise chart's camera offset so high read noise doesn't clip at 0
  
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- docs: play/stop button for the noise chart (new noise at 10 fps)
  
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- docs: describe detectors and modalities without advising which hardware to use
  
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- docs: rename the detector pipeline section
  
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- docs: make the sCMOS pixel-variation limitation a danger admonition
  
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- docs: neutral wording for the EMCCD/sCMOS SNR stat
  
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- docs: remove the simulated SNR dots from the detector chart (a test, not a figure)
  
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- docs: sCMOS starts at 1 e⁻ read noise in the detector charts
  
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- docs: fixes from the prose check (failing command, saturation and spot power, readout order, caches, run_batch, irradiance range)
  
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- docs: chart physics into physics/ with tests, presets and lens from exported data
  
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- skills: update check-js-physics and check-docs-prose from a test run
  
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- docs: tighten the advice search in check-docs-prose; reflow saving.md
  
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- Merge branch 'main' into docs-zensical
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- docs: describe max_psf_radius_aus="auto" (#158)
  
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Commits

Commits on Oct 11, 2026