redsun-mimir 0.2.0

Plugin bundle for the OpenUC2 'Mimir' microscope

redsun-mimir

Bundle of redsun components for the openUC2 "Mimir" microscope

About mimir

Mimir is the codename for an in-development portable interferometric scattering microscope (iSCAT), with an hardware controller developed by openUC2. It employs pymmcore-plus for camera control and pyserial for motor and laser control.

redsun-mimir is a bundle of components developed to target the specific hardware and software requirements for real-time acquisition with said microscope.

[!NOTE] This bundle has been used as a staging ground for development in cohesion with the main framework. Some components may be moved to redsun itself to be provided as built-in functionalities. Expect breaking changes as the framework evolves.

[!WARNING] The youseetoo module has not been fully tested and there is currently no known way of testing it in a continous integration. Ensure you can pre-emptively test the components locally.

Installation

It is strongly reccomended to install redsun-mimir in a virtual environment.

uv (reccomended)

Be sure to install uv first.

# create the venv
uv venv --python 3.10

# activate the environment in...
# ... linux
source .venv/bin/activate

# ... windows
.venv\Scripts\activate

uv pip install redsun-mimir

pip

You should have Python installed in your machine.

# create the venv
python -m venv .venv

# activate the environment in...
# ... linux
source .venv/bin/activate

# ... windows
.venv\Scripts\activate

pip install redsun-mimir

Installing from source

redsun-mimir is developed via uv; you can clone the repository and install development dependencies:

git clone https://github.com/redsun-acquisition/redsun-mimir

cd redsun-mimir

uv sync

Running a simulator container

redsun-mimir comes with a simple simulation environment with simulated devices for demonstration purposes.

To run it, you have to:

1. install the package in your virtual environment by adding the sim optional dependencies;
2. run mmcore install (or alternatively one of the methods described here).
3. run the container via mimir sim.

uv (reccomended)

# in your virtual environment
uv pip install redsun-mimir[sim]

# install micro-manager device adapters
mmcore install

# run the example container via command line
mimir sim

pip

# in your virtual environment
pip install redsun-mimir[sim]

# install micro-manager device adapters
mmcore install

# run the example container via command line
mimir sim

Features

• Live data capture.
• Median computation based on square-scan movement for background noise reduction following the procedure described in this paper.
• Image visualization leveraging napari.
• Data storage in Zarr v3 format via acquire-zarr.
• Manual control of light source and motor drivers.
• Fully extensible via additional components following the redsun framework.

Contributing

Contributions are very welcome. Tests can be run with pytest, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the Apache Software License 2.0 license, redsun-mimir is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.