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3 detection filter upgrades - #4

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3-detection-filter-upgrades
Jul 27, 2026
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3 detection filter upgrades#4
jhohlbein merged 7 commits into
mainfrom
3-detection-filter-upgrades

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@kjamartens

@kjamartens kjamartens commented Jul 27, 2026

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See issue #3

kjamartens and others added 6 commits July 27, 2026 12:15
@kjamartens
gitignore vscode ignoring (#3)
8787d6e
@kjamartens
Added real-time update for showing detection/fitting changes (#3)
a6c0be4 
Upon changes in fit/detection method, or upon changing the raw frame, detection/fit is run for this frame and displayed to the user.
@kjamartens
Green boxes size managed by fit radius (#3)
7643730 
Fit radius now dictates the detection-green-boxes in live preview
@kjamartens
Changed scroll-wheel behaviour on raw data (#3)
c9f676d 
Scroll wheel now scrubs through data, ctrl+scroll wheel zooms.
Scroll wheel also works on the slider below.
Tested on windows+firefox
@kjamartens @claude
Split detection filter params per method with show/hide
a35cb48 
Threshold (k·sigma_noise) and Exact band-pass were shared across the
Wavelet and DoG filters even though they don't mean the same thing (or
apply at all) for each. Give each method its own field
(detection_wavelet_thr / detection_DoG_thr / detection_DoG_exactbp),
show only the relevant row for the selected filter, and thread the
rename through settings save/load and live-preview wiring. Prep work
for adding the Uniform Box Filter detection method.

Refs #3

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
@kjamartens @claude
Add uniform box filter detection method
fe5d037 
Implements the box-averaging detection from Huang, Schwartz, Byars &
Lidke (2011): difference of two box filters sized off sigma_PSF,
thresholded on plain intensity rather than k*sigma, with local maxima
found via a sigma_PSF-sized square dilation instead of the fixed 3x3
window wave/dog use. detectSpots() is now the single dispatch point
(main thread + worker) picking band-pass + maxima-finder per method.

The dilation's sliding-max (maxH/maxV) initially recreated a closure
per row/column and used modulo in the hot loop, making box detection
much slower than DoG; rewrote it closure-free with persistent scratch
buffers, bringing it in line with DoG's per-frame cost.

Also documents the live-preview mechanism (showFrame/detectSpots reuse
for the real-time scrub preview) in CLAUDE.md.

Refs #3

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
@kjamartens kjamartens linked an issue Jul 27, 2026 that may be closed by this pull request
Detection filter upgrades #3
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@kjamartens

kjamartens commented Jul 27, 2026

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Changed scroll and ctrl-scroll behavior as requested by JH

jhohlbein
jhohlbein approved these changes Jul 27, 2026
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Reviewed the full diff, syntax-checked the branch, numerically validated the new detection path, and checked for regressions. Solid, merge-ready.

Verified

  • Box-filter math is correct: boxH/boxV normalise (nm=1/(2r+1)), so uniformBP is a true difference of box means — strongly positive at spots, ~0 at background.
  • The deque dilation (maxH/maxV) is exact: matched a brute-force sliding-window max with 0 mismatches; findMaximaUniform found precisely the planted spot.
  • Worker gotcha handled: new state in WORKER_PRELUDE, all 8 new functions in workerSource(), and the ping self-test exercises detectSpots(...,'box',...) (so any stringification slip falls back cleanly).
  • Rename complete — no stale $('thr')/$('exactbp') references.
  • No conflict with 0.9.0: the ctrl+wheel scrub is inside if(!nav.full()), so it never fires while a histogram/profile plot owns the raw panel.
  • Full-file syntax OK; CLAUDE.md / help text / Huang 2011 reference all added well.

Minor (non-blocking) follow-ups

  1. SETTING_IDS dropped thr/exactbp, so a settings.json saved by ≤0.9.0 won't restore those two fields — consider aliasing the old keys on load.
  2. Box maxima are non-strict (filt[i]===dilation) vs. the strict > used by wavelet/DoG — theoretical plateau duplicates only (won't happen on real float data).
  3. Live preview re-detects+re-fits the whole frame on the main thread per scrub/setting change (incl. MLE); coalesced so it won't queue, but may feel heavy on dense stacks under MLE.

Approving.

@jhohlbein
jhohlbein merged commit 63eb601 into main Jul 27, 2026
jhohlbein added a commit that referenced this pull request Jul 27, 2026
@jhohlbein @claude
Release 0.9.1: detection-filter upgrades (uniform box + real-time pre…
7699232 
…view)

Version bump + docs for the merged PR #4: adds a uniform box detection filter
(Huang et al. 2011) behind a single detectSpots() dispatch, per-method threshold
fields, a real-time scrubbed-frame preview toggle, and a raw-panel scroll rework
(wheel = zoom, ctrl+wheel = scrub). Patch release — no new DOI.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
jhohlbein added a commit that referenced this pull request Aug 8, 2026
@jhohlbein @claude
build 2026-08-08k: docs cleanup, Acknowledgements section, FRC harmon…
8fa3af1 
…ic-aliasing note

- webSMLM.html: copyright/attribution "Johannes Hohlbein" -> "Hohlbein et al."
  (top-of-file comment, header, Help & guide License section); new
  Acknowledgements section in Help & guide crediting Koen J. A. Martens'
  verified PR #4 contributions (uniform box-filter detection, Real-time
  update toggle, wheel-zoom/ctrl+wheel-scrub scroll rework, ROI box sizing).
- experimental_data/README.md: note that FRC peaks at 40/20 nm on the
  GATTA-PAINT dataset are harmonics of the 80 nm ruler spacing, not a bug.
- README.md: fix stale button names (Run localisations -> Localize, Display
  table -> View data + filtering), same copyright change, mention the crop
  tool and temporal clustering (previously undocumented), qualify the single
  "~350k loc/s" figure as Phasor-specific and a ceiling not a typical rate.
- CLAUDE.md: correct line count (~4000 -> ~5800), drop the dead reference to
  REFACTOR_PLAN.md's removed "Shipped" table, drop the dangling reference to
  the removed Nile Red section.
- docs/REFACTOR_PLAN.md: drop the CSV-export-of-filtered-subset roadmap item
  (already shipped via renderLocs-based export), correct stale line count.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
jhohlbein added a commit that referenced this pull request Aug 15, 2026
@jhohlbein @kjamartens @claude
Release 0.10.2: gain/offset estimation (PCFO), simulation camera mode…
2e87f36 
…l, FTM mobile-OOM fix

Clears the -dev marker (v0.10.2-dev · build 2026-08-15h -> v0.10.2) and
brings docs up to date for release:

- CHANGELOG.md gets the full 0.10.2 entry.
- docs/REFACTOR_PLAN.md's photon-calibration roadmap item trimmed: PCFO
  (single-image gain/offset estimation) shipped, per-pixel sCMOS
  calibration maps stays the open remainder.
- README.md gains a "What it does" bullet and reference for PCFO gain/offset
  estimation, and the ADU/gain known-limitation note now points to it.
- docs/DOCUMENTATION.md's line-reference note bumped to v0.10.2.
- In-app Help & guide: new References entry for the PCFO paper (Heintzmann,
  Relich, Nieuwenhuizen, Lidke & Rieger, arXiv:1611.05654 — verified title
  via the arXiv listing itself, not invented) and a second Acknowledgements
  line crediting Koen J. A. Martens' PR #5 contribution, alongside his
  existing PR #4 credit.
- CITATION.cff version/date-released bumped to 0.10.2 / 2026-08-15; authors
  list unchanged (Hohlbein only) — PR contributions are credited in
  Acknowledgements, not software citation authorship, matching the existing
  PR #4 precedent.

Verified end-to-end in a real browser after all doc/version edits: Simulate
-> Estimate -> Transfer estimates -> Localize (FTM on) completes cleanly,
version pill reads v0.10.2, no console/page errors.

Co-Authored-By: Koen J.A. Martens <32260034+kjamartens@users.noreply.github.com>
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Detection filter upgrades

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