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MM_python_SMLM_localizer

This is the Git repository for creating a Micro-manager plugin to run a custom python script for localizing and visualizing SMLM images

Setting up

The plugin is developed in Netbeans 15 with Java 8 (as required my micro-manager) and tested on Micro-manager 2.0 stable and 2.0.3 (nightly) versions. Please follow the micro-manager guidelines for writing a plugin. We suggest using the Netbeans IDE.

The Python script is tested with Python 3.12.7. I would suggest you use Anaconda / Miniconda.

Usage (Python)

  1. Install all the dependencies. Anaconda should have them by default, but please install them if something is unavailable.

  2. Currently, the script (placed in runLocalizer/script.py) is designed to localize the detected PSFs using a phasor based method, you can modify it according to your method of choice by redefining the process_image function and editing the main function accordingly.

Usage (Java)

  1. Open the project (runLocalizer) in Netbeans, provide the location of the python code in the runLocalizer.java code, compile the plugin and copy the JAR file from the dist folder to Micro-manager install folder > mmplugins.

  2. Start Micro-manager.

  3. When you are ready to acquire images, start MDA and select save images > select 'separate image files'. Remember the saving location.

  4. Once acquisition starts, go to Plugins > Acquisition tools > Run Python localizer script.

    • select the directory where images are being saved.
    • enter the number of images to process and press OK.

  5. The results will be showing up as below:

Thank you,

Pranjal Choudhury February 2025