OpenFlexure Microscope Software

Quickstart

A general user-guide on setting up your microscope can be found here on our website. This includes basic installation instructions suitable for most users.

Full developer documentation can be found on ReadTheDocs. This includes installing the server in a mode better suited for active development.

Developer installation

git clone https://gitlab.com/openflexure/openflexure-microscope-server.git
poetry install
poetry run build_static

Pre-commit hooks

We make use of pre-commit hooks to run code analysis before committing to the codebase.

The simplest way to ensure this works is to install pre-commits into your global Python environment:

pip3 install pre-commit
pre-commit install

Alternatively, you can work within the Poetry project's virtual environment where pre-commit will already be installed as a developer dependency.

Finally, to run all analysis within installing pre-commits to Git, you can run pre-commit run.

Node installation

Note, building the static interface will require a valid Node.js installation
To build on a Raspberry Pi:
- curl -sL https://deb.nodesource.com/setup_14.x | sudo bash -
- sudo apt install nodejs

Distributing

mkdir -p dist
tar -c --exclude-vcs --exclude-from .tarignore -vzf dist/openflexure-microscope-server.tar.gz .

Docker

We don't use docker to distribute the server application due to the number of system-level permissions it would need, and the fact that docker mounts break the autostorage extension. If you really want to use docker though, after building the image on your pi you need to start the container with the following flags:

docker run --privileged -v /opt/vc:/opt/vc --env LD_LIBRARY_PATH=/opt/vc/lib --device /dev/vchiq --publish 5000:5000

Build-system

As of 1.0.0b0, we're using Poetry to manage dependencies, build, and distribute the package. All package information and dependencies are found in pyproject.toml, in line with PEP 518. If you're developing this package, make use of poetry.lock to ensure you're using the latest locked dependency list.

Microscope plugins

The Microscope module, and Flask app, both support plugins for extending lower-level functionality not well suited to web API calls. This plugin system is still in fairly early development, and is not yet properly documented. The current documentation can be found here.

Running tests through the PTVSD remote debugger (port 3000)

From the openflexure-microscope-software directory, run python3 -m ptvsd --host 0.0.0.0 --port 3000 --wait tests/test_camera.py

Credits

Piexif

The microscope server includes a forked copy of hMatoba's Piexif, licensed under the MIT License.

Video streaming

Based on supporting code for the article video streaming with Flask and its follow-up Flask Video Streaming Revisited.

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