GRANA

GRANA (Graphical Recognition and Analysis of Nanostructural Assemblies) is an an AI-enhanced, user-friendly software tool that recognizes grana on thylakoid network electron micrographs and generates a complex set of their structural parameters measurements.

It is described in the article: "GRANA: An AI-based tool for accelerating chloroplast grana nanomorphology analysis using hybrid intelligence"

Website

More information about GRANA, including example dataset, can be found at GRANA website.

Demo

Demo version of GRANA is available at Hugging Face Spaces. Using demo version, you can analyze up to 5 images at once.

Installation and usage

Running as a pre-build Docker container

The recommended way to run GRANA is to use the Docker container form repository.

To run the container, use the following command:

docker run -p 7860:7860 mbuk/grana

After running the command, you can access the GRANA interface at http://localhost:7860.

Building container locally

If you prefer to build the container locally, use the following commands:

1. Clone the repository:

   git clone git@github.com:center4ml/GRANA.git
   cd GRANA
   

2. Build the Docker image:

   docker build -t <image-name> .
   

   Where <image-name> is the name of your choice, e.g. "grana"

3. Run the Docker container:

   docker run -p 7860:7860 <image-name>
   

   After running the command, you can access the GRANA interface at http://localhost:7860.

Running from Source

To run the project locally, ensure you have Python 3.9+ installed and follow these steps:

1. Clone the repository:

   git clone git@github.com:center4ml/GRANA.git
   cd GRANA
   

2. Install the dependencies:

   pip install -r requirements.txt
   

3. Start the Gradio interface:

   python app.py
   

The Gradio interface should now be running locally and accessible at http://localhost:7860.

Examples

Sample images for processing with the GRANA tool are stored in the sample_images directory. Each image has a scale of 1.298 pixels/nm, as indicated in the file names.

Citation

Article: "GRANA: An AI-based tool for accelerating chloroplast grana nanomorphology analysis using hybrid intelligence"

@article{bukat2025grana,
  title={GRANA: An AI--based tool for accelerating chloroplast grana nanomorphology analysis using hybrid intelligence},
  author={Bukat, Alicja and Bukowicki, Marek and Bykowski, Micha{\l} and Kuczkowska, Karolina and Nowakowski, Szymon and {\'S}liwi{\'n}ska, Anna and Kowalewska, {\L}ucja},
  journal={Plant Physiology},
  volume={198},
  number={2},
  pages={kiaf212},
  year={2025},
  publisher={Oxford University Press US}
}