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Fibermorph dev - #22

Closed

ezhil384 wants to merge 68 commits into

lasisilab:mainfrom

ezhil384:fibermorph-dev

Closed

Fibermorph dev#22
ezhil384 wants to merge 68 commits into
lasisilab:mainfrom
ezhil384:fibermorph-dev

Commits on Nov 7, 2025
- Move modified GUI app to development branch
  tinalasisi
  committed
  1703d6b
- Improve image validation and error handling
  tinalasisi
  committed
  6bde71e
Commits on Mar 14, 2026
- Added docker
  ezhil384
  committed
  13b43a9
Commits on May 15, 2026
- Updated v2 with SAM
  Abhiraj Ezhil
  committed
  69f15d4
- fix: resolve CI failures and Streamlit Cloud deployment errors
  
  Abhiraj Ezhil
  and
  claude
  committed
  8590977
- fix: clear packages.txt to resolve Streamlit Cloud apt dependency conflict
  
  Abhiraj Ezhil
  and
  claude
  committed
  3c10b42
- fix: empty packages.txt completely — Streamlit Cloud treats comments as package names
  Abhiraj Ezhil
  committed
  d0b1ceb
- fix: widen version upper bounds for Python 3.14 wheel compatibility
  Abhiraj Ezhil
  committed
  5493535
- fix: correct segment_section keyword args in GUI helper
  Abhiraj Ezhil
  committed
  eadfc25
- fix(tests): update tests to match refactored v2 API
  
  Copilot
  and
  ezhil384
  authored
  5388b08
- Merge pull request #2 from ezhil384/copilot/create-new-tests-for-refactored-version
  ezhil384
  authored
  48dce86
- Merge pull request #1 from ezhil384/feature/v2-enhanced-analysis
  ezhil384
  authored
  d06b3ec
Commits on Jul 3, 2026
- Merge PR #16 from ezhil384/fibermorph (fibermorph-v2) into dev
  
  tinalasisi
  and
  claude
  committed
  03c714d
- Fix TestListImages to create valid TIFFs; add invalid-file test
  
  tinalasisi
  and
  claude
  committed
  66d0b5b
- Fix mechanical defects found in fork review
  
  tinalasisi
  and
  claude
  committed
  2c8178e
- Packaging fixes from fork review
  
  tinalasisi
  and
  claude
  committed
  372038d
- CI: run tests on pushes to fibermorph-dev
  
  tinalasisi
  and
  claude
  committed
  38ea921
Commits on Jul 4, 2026
- Fix section-resolution mislabel (µm/px -> px/µm) and warn on empty masks
  
  tinalasisi
  and
  claude
  committed
  55105d9
- Quick Test: drop filename-based grouping; make single-image work
  
  tinalasisi
  and
  claude
  committed
  d91f67a
- Separate image analysis from data analysis: per-image only, no grouping
  
  tinalasisi
  and
  claude
  committed
  49b7dd2
- GUI: document naming, one ungrouped histogram, and resolution-aware downsampling
  
  tinalasisi
  and
  claude
  committed
  20c2c8a
- Drop filename parsing entirely: per-image output keeps only source_file
  
  tinalasisi
  and
  claude
  committed
  2b7801d
- GUI: split Cross-Section and Curvature into separate tabs
  
  tinalasisi
  and
  claude
  committed
  c001615
- Fix pre-test bugs found in GUI review
  
  tinalasisi
  and
  claude
  committed
  00adca9
- Accept resolution in either direction (px/unit or unit/px)
  
  tinalasisi
  and
  claude
  committed
  6db76e6
- Collapse cluster tabs into one 'Run at scale' helper; scrub personal info
  
  tinalasisi
  and
  claude
  committed
  333022b
- Explain Taubin window & CLAHE; rename 'Run at scale' -> 'Run Remote'
  
  tinalasisi
  and
  claude
  committed
  43770e0
- Curvature GUI: surface per-fragment length + curvature; refocus metrics
  
  tinalasisi
  and
  claude
  committed
  cb4f098
- Add Run Local tab + local folder-path mode for large images
  
  tinalasisi
  and
  claude
  committed
  6a4b2ed
- Remove the curvature diameter metric (not trusted)
  
  tinalasisi
  and
  claude
  committed
  68617b3
- Curvature: per-sample panelled histograms + US spelling
  
  tinalasisi
  and
  claude
  committed
  374a31a
- Curvature per-sample panels: share x-axis per metric column
  
  tinalasisi
  and
  claude
  committed
  34164c0
- Update .gitignore
  tinalasisi
  committed
  d377a3e
- Reskin GUI in the Lasisi Lab design system (sidebar console)
  
  tinalasisi
  and
  claude
  committed
  60ea4c2
- Nav: elegant SVG glyphs (no emoji), more top room, US spelling
  
  tinalasisi
  and
  claude
  committed
  04f7d51
- Sidebar: 20% narrower and nav content flush-left
  
  tinalasisi
  and
  claude
  committed
  fde7101
- Nav sub-labels, pink wand Generate button
  
  tinalasisi
  and
  claude
  committed
  8deb8d3
- Docs: refresh README/CHANGELOG, add ROADMAP; make fibermorph-gui first-run clean
  
  tinalasisi
  and
  claude
  committed
  7462579
Commits on Jul 9, 2026
- chore: drop unused 58MB SimArcData fixture; gitignore *.tif(f)
  
  tinalasisi
  and
  claude
  committed
  7162bc9
Commits on Oct 1, 2026
- Merge main into fibermorph-dev
  
  tinalasisi
  and
  claude
  committed
  117c581
- chore: normalize line endings to LF
  
  tinalasisi
  and
  claude
  committed
  1e2ff52
- feat(gui)!: require --local for fibermorph-gui local mode
  
  tinalasisi
  and
  claude
  committed
  3655751
- fix(gui)!: hide the SAM2 checkpoint path from hosted visitors
  
  tinalasisi
  and
  claude
  committed
  3d3a750
- fix(gui): save uploads under generated names, not client filenames
  
  tinalasisi
  and
  claude
  committed
  5dbfefc
- fix(gui): warn when local mode is given an empty --server.address
  
  tinalasisi
  and
  claude
  committed
  e246213
- fix(curvature)!: freeze the scikit-image 0.16.2 Frangi filter
  
  tinalasisi
  and
  claude
  committed
  674f5b7
- fix(gui): show the upload cap the server actually enforces
  
  tinalasisi
  and
  claude
  committed
  6bed4ed
- fix(curvature)!: restore whole-hair mode and per-hair test output
  
  tinalasisi
  and
  claude
  committed
  8791112
- fix(gui): do not imply SAM2 works when only a checkpoint file exists
  
  tinalasisi
  and
  claude
  committed
  1e3c1aa
- docs(changelog): list the SAM2 checkpoint change under Breaking Changes
  
  tinalasisi
  and
  claude
  committed
  d3f6dc8
- test(curvature): add golden tests against original v0.3.1 output
  
  tinalasisi
  and
  claude
  committed
  d383b0a
- Merge: curvature reproduces the original v0.3.1 method again
  
  tinalasisi
  and
  claude
  committed
  beff8a2
- Merge: hosted-mode safety fixes for the Streamlit GUI
  
  tinalasisi
  and
  claude
  committed
  5faf751
- docs: correct SAM2 checkpoint and release wording; fix a test
  
  tinalasisi
  and
  claude
  committed
  b7da183
- fix(cli): read --window_size as numbers so mm and 50.0 stop crashing
  
  tinalasisi
  and
  claude
  committed
  72f2653
- fix(cli): document the 10 px window floor and tidy --window_size errors
  
  tinalasisi
  and
  claude
  committed
  f06a78f
- refactor(curvature)!: remove the CLAHE preprocessing option
  
  tinalasisi
  and
  claude
  committed
  ae0ca66
- refactor(curvature)!: remove the extended curvature metrics option
  
  tinalasisi
  and
  claude
  committed
  9651767
- docs: document removal of CLAHE and extended curvature options
  
  tinalasisi
  and
  claude
  committed
  8c17805
- fix(cli): refuse out-of-range --jobs, resolutions and size limits
  
  tinalasisi
  and
  claude
  committed
  068b90d
- fix(cli): refuse a --window_size longer than 1,000,000,000 pixels
  
  tinalasisi
  and
  claude
  committed
  10eda5b
- Merge: remove the CLAHE and extended curvature options
  
  tinalasisi
  and
  claude
  committed
  c5fd82f
Commits on Oct 2, 2026
- Merge: fibermorph CLI reads --window_size as numbers
  
  tinalasisi
  and
  claude
  committed
  61141ae
- fix(cli): cap --jobs at the CPU count; keep GUI scripts valid
  
  tinalasisi
  and
  claude
  committed
  899f533
Commits on Oct 5, 2026
- feat(gui): show SAM2 as unavailable on the hosted app and point to local/cluster
  
  Abhiraj Ezhil
  and
  claude
  committed
  632edd7
- fix(sam2): make --use-sam2 load SAM2 instead of silently using watershed
  
  Abhiraj Ezhil
  and
  claude
  committed
  af8b8e7
- Merge pull request #3 from ezhil384/fix/cli-sam2-config
  ezhil384
  authored
  999d43d
- Merge pull request #4 from ezhil384/fix/hosted-sam2-unavailable
  ezhil384
  authored
  ece31e2

Commits

Commits on Nov 7, 2025

Commits on Mar 14, 2026

Commits on May 15, 2026

Commits on Jul 3, 2026

Commits on Jul 4, 2026

Commits on Jul 9, 2026

Commits on Oct 1, 2026

Commits on Oct 2, 2026

Commits on Oct 5, 2026