Issues

• SW-06 item 25: GUI: curvature on a large image (20 MP) needs ~4.4 GB and gets the app killed on a login node, a small job or a hosted app

  bug
  lasisilab/fibermorph#48 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 24: Files with the same name but different extensions get the same ID in the CLI output, with no warning

  lasisilab/fibermorph#47 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 23: Every cross-section TIFF logs "skimage failed to read …, falling back to PIL"

  lasisilab/fibermorph#46 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 22: The "watershed" fallback doesn't use watershed: it's Otsu thresholding + opening/closing + connected regions

  documentation
  lasisilab/fibermorph#45 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 21: README's SAM2 checkpoint step (mkdir -p fibermorph/checkpoints) only works from a source checkout

  documentation
  lasisilab/fibermorph#44 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 20: README and Run Local say pip install "fibermorph[gui]", but PyPI has 1.0.1, so users get the old version

  documentation
  lasisilab/fibermorph#43 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 19: Run Remote: the SAM2 script runs curvature on the GPU node and starts N SAM2 workers on one GPU

  lasisilab/fibermorph#42 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 18: --extended-features output has no minor/major axis (min/max diameter) columns

  enhancement
  lasisilab/fibermorph#41 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 17: curvature_summary_data_*.csv has a stray unnamed first column of zeros

  bug
  lasisilab/fibermorph#40 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 16: GUI "Median Curvature" (curv_median) is the CLI's curv_mean_median, not curv_median_median

  documentation
  lasisilab/fibermorph#39 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 15: CLI and GUI defaults differ (cross-section min diameter 20 vs 30 µm; curvature window whole-hair vs 50 px)

  documentation
  lasisilab/fibermorph#38 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 14: n_radial_peaks doesn't wrap around 0°/360°: a lobe at 0° is missed or counted twice

  bug
  lasisilab/fibermorph#37 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 13: Shape classifier labels moderately lobed, triangular and egg-shaped outlines as Circular/Irregular

  lasisilab/fibermorph#36 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 12: Circularity, convexity and perimeter are biased by the stair-stepped pixel outline (a perfect circle scores 0.90)

  bug
  lasisilab/fibermorph#35 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 11: Threshold ("watershed") fallback measures a background speck instead of the section (143506_A_5: 128 µm², confidence 0.19)

  bug
  lasisilab/fibermorph#34 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 10: CLI: skipped images are reported with internal error text, reasons and file names on separate lines, and no summary at the end

  lasisilab/fibermorph#33 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 09: "No cross-section was detected" always blames the resolution, even when the resolution is right

  lasisilab/fibermorph#32 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 08: --extended-features silently switches to a different segmenter, changing which images get a result and their area

  bugdocumentation
  lasisilab/fibermorph#31 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 07: GUI and CLI give different cross-section results for the same images and settings (GUI downsamples to ~2 px/µm first)

  bug
  lasisilab/fibermorph#30 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 06: The CLI reads only .tif/.tiff (case-sensitive), although the GUI accepts PNG and JPEG

  bug
  lasisilab/fibermorph#29 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 05: An empty or mistyped input folder crashes with a pandas traceback (No objects to concatenate)

  bug
  lasisilab/fibermorph#28 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 04: radial_mean_mu, radial_std_mu, radial_min_mu, radial_max_mu are not in µm (pixels × px/µm instead of ÷)

  bug
  lasisilab/fibermorph#27 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 03: Hosted app runs an old version: it shows and lets visitors edit the server's SAM2 checkpoint path

  lasisilab/fibermorph#26 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 01: --use-sam2 never runs SAM2: an empty --sam2-cfg makes SAM2 fail to load and every image silently uses watershed

  bug
  lasisilab/fibermorph#25 · Filter by author ezhil384 opened on Oct 16, 2026

• SW-06 item 02: Hosted app: the SAM2 switch can be turned on, but the app has no GPU and silently segments with watershed

  bug
  lasisilab/fibermorph#24 · Filter by author ezhil384 opened on Oct 16, 2026