BioPic LM

BioPic LM is a lightweight cross-platform desktop application for building reproducible, publication-quality microbiological figures from light-microscopy images.

Beta release: BioPic LM is currently pre-release software. Expect bugs and incomplete workflows.

Milestones 1 through 8 provide the runnable application shell, project/document model, dependency invalidation, atomic project persistence, logging, baseline tests, image import, stack import, metadata inspection, thumbnail/canvas workspaces, project save/load for imported sources, and an independent focus-stacking engine, non-destructive image-editing foundations, and measurement/calibration/scale-bar models, annotations, figure boards, and export/preflight foundations.

Technology

• Python 3.12+
• PySide6 / Qt 6 for native Windows and Linux desktop UI
• NumPy, SciPy, Pillow, tifffile, imageio for scientific imaging foundations
• SQLite-ready project metadata with human-readable JSON manifests
• pytest, ruff, mypy for quality checks
• PyInstaller planned for Windows and Linux packaging

Run

python -m pip install -e .[dev]
biopic-lm

If PySide6 is not installed, non-GUI tests and model code still run.

Test

$env:PYTEST_DISABLE_PLUGIN_AUTOLOAD="1"
python -m pytest -q
ruff check .
mypy src

Current Scope

The current focus stacker supports translation alignment, Laplacian/modified Laplacian/Tenengrad/local-variance focus metrics, regularized focus maps, smooth weighted blending, halo suppression, depth-map output, and parameter provenance. Rotation/scale alignment and manual mask painting are planned follow-ups.

Beta Limitations

• Stack from Video is experimental and has not been fully tested.
• Stitch Images is experimental and has not been fully tested.
• Some UI tools and image-editing operations may still have bugs.
• Presets created locally through the app are user settings or project data; they are not bundled into the source repository unless exported or saved in a project file.

Distribution

Packaged application builds are kept separate from the source repository. Local build/ and dist/ folders are ignored and should not be committed. Upload packaged .zip builds through GitHub Releases instead.

See docs/DISTRIBUTION.md for the exact source upload and release workflow.