Developer documentation

Generated from docs/developers/README.md in fibsem-os at build time. Edit it there; changes here are overwritten.

Documentation for changing or extending fibsemOS. The user guide for operating the application is at fibsemos.org/docs .

Page	Contents
Getting started as a developer	Repository layout, running the application against the simulator, running tests, and which extension point applies to a given goal.
Contributing	Pull request size, the Python version floor, formatting, tests, and network rules.
Extending fibsemOS	Scripts, plugins (patterns, strategies, tasks), workflow tasks, and microscope backends.
Scripting experiments	Reading and modifying experiment data from Python, in a notebook or from the application.
The simulator	What the Demo microscope images, the scene configuration keys, and how the figures are generated.
The screenshot harness	How the user guide’s screenshots are rendered from the application, and how to add a page.
AGENTS.md	Conventions for coding agents. Contributing applies in full; this file adds what is specific to agents.

Developers and coding agents use the same pages. AGENTS.md and the skills under .claude/skills/ are entry points into them, not separate documentation.

Generated content

Two of these pages are partly generated, and the code examples in a third are executed by the test suite:

The figures and the key table in simulator.md are written by render_simulator_examples.py from the scene’s defaults. Re-run it after changing the simulator.
The user guide’s screenshots are written by render_user_guide.py from the running application. A page state that names a widget that no longer exists fails the run.
The example scripts in SCRIPTING.md run in the test suite against a real experiment and the simulator.

A change to something one of these pages describes should update the page in the same pull request.