ImSTORM

A Python application for 2D image reconstruction of single molecular localization data.

Features

• SMLMS Image generation /Simulation
• SMLMS reconstruction based on the microeye package
• Integration with arkitekt-next for server-based workflows
• Docker support for easy deployment

Requirements

• Docker (for containerized deployment)
• Python 3.12+ (for local development)
• Dependencies listed in requirements.txt

Installation

Using Devcontainer

This repository comes with a devcontainer setup for easy deployment. To run the application in a container, open the repository in Visual Studio Code and click on the "Reopen in Container" button. Otherwise you will find the Dockerfile in the .arkitekt_next/flavours/vanilla directory, which is build to run the application.

Then in the container terminal, run the following command to start the application:

arkitekt-next run dev

Using Python

1. Clone the repository:

2. Create a virtual environment:

   python -m venv venv
   source venv/bin/activate  # On Windows, use venv\Scripts\activate

3. Install dependencies:

   pip install -r requirements.txt
   git clone https://github.com/openUC2/microEyeUC2/
   cd microeye 
   git checkout noqt
   pip install --no-deps 

4. Run the script:

   arkitekt-next run dev

Contributing

Contributions are welcome! Please follow these steps:

1. Fork the repository.
2. Create a feature branch.
3. Commit changes and push to your fork.
4. Open a pull request.

License

This project is licensed under the MIT License. See LICENSE for details.