BioPic LM

BioPic LM is a desktop application for organizing light-microscopy images and building reproducible, publication-ready biological figure panels.

This repository contains the source code. Packaged Windows builds are published separately as GitHub Release assets.

Beta Status

BioPic LM 0.1.0 beta 1 is a pre-release build. It is intended for early testing, not final production work.

Known beta limitations:

• Stack from Video is experimental and not fully tested.
• Stitch Images is experimental and not fully tested.
• Some image-editing tools and UI workflows may still contain bugs.
• Performance for very large images can still vary by operation and hardware.

When publishing this version on GitHub, mark the release as a pre-release.

Main Features

• Import common microscopy image formats, including TIFF and RAW when rawpy is installed.
• Manage image sources, image stacks, metadata, measurements, annotations, and figure boards in one project.
• Create focus stacks with alignment, focus metrics, depth maps, and provenance.
• Apply non-destructive edit layers, adjustment layers, filters, selections, scale bars, and annotations.
• Build figure boards with panel layout, labels, spacing, captions, and export support.
• Save projects as human-readable .biopic.json manifests.

Experimental Features

• Stack from Video: import video, cut retained sections, extract frames, and create an image stack.
• Stitch Images: combine overlapping standalone images into a stitched result.

These workflows are included for testing, but they should not be considered stable yet.

Requirements

For source/development use:

• Python 3.12 or newer
• Windows or Linux
• PySide6 / Qt 6
• NumPy, SciPy, Pillow, tifffile, imageio, OpenCV, scikit-image
• Optional RAW support: rawpy

For end users, a packaged release build should run without installing Python.

Run From Source

From the repository root:

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

The legacy command alias also works:

biopic

Tests And Checks

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

Some test workflows may still need local cleanup during beta development.

Build A Windows Distribution

Install packaging dependencies:

python -m pip install -e .[packaging,raw]

Build the app:

python -m PyInstaller BioPicLM.spec --clean --noconfirm

The packaged application is created at:

dist/BioPic LM/

Create a release ZIP:

Compress-Archive -Path "dist\BioPic LM" -DestinationPath BioPic-LM-windows-x64.zip -Force

Do not commit build/, dist/, or release ZIP files. Upload the ZIP as a GitHub Release asset instead.

Presets

User-created presets are not automatically bundled into a source upload or binary release.

Preset storage depends on how the preset was created:

• Project-specific presets are saved inside .biopic.json project files.
• Persistent user presets are stored in local application settings.
• Bundled presets must be exported or added explicitly under src/biopic/presets/ before packaging.

At the moment, src/biopic/presets/ does not contain user preset data.

GitHub Release Workflow

Commit source code to the repository:

git status
git add .gitignore README.md AUTHORS NOTICE docs src tests icons packaging pyproject.toml setup.py BioPicLM.spec LICENSE COPYING
git commit -m "Prepare BioPic LM beta source repository"
git branch -M main
git remote add origin https://github.com/YOUR_USER_OR_ORG/biopic-lm.git
git push -u origin main

Tag the beta release:

git tag v0.1.0-beta.1
git push origin v0.1.0-beta.1

Create a GitHub Release for v0.1.0-beta.1, mark it as a pre-release, and attach BioPic-LM-windows-x64.zip.

Repository Layout

src/biopic/       Application source code
tests/            Tests and regression checks
docs/             Architecture, licensing, and release notes
icons/            Application icon and logo assets
packaging/        PyInstaller launcher and packaging helpers
BioPicLM.spec     PyInstaller build specification

Licensing And Attribution

BioPic LM is distributed under GPL-3.0-or-later.

GIMP and RawTherapee are used only as behavior and user-interface references. No GIMP or RawTherapee source file, icon, brush, cursor, preset, or other asset has been copied into this repository.

See:

• LICENSE
• COPYING
• NOTICE
• AUTHORS
• docs/THIRD_PARTY_CODE.md