https://github.com/henriqueslab/sred

Structural Repetition Detector (SReD) - Quantitative mapping of molecular complexes
https://github.com/henriqueslab/sred

Last synced: 9 months ago
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Structural Repetition Detector (SReD) - Quantitative mapping of molecular complexes

• Host: GitHub
• URL: https://github.com/henriqueslab/sred
• Owner: HenriquesLab
• License: mit
• Created: 2021-04-20T10:52:34.000Z (about 5 years ago)
• Default Branch: main
• Last Pushed: 2025-02-18T12:30:58.000Z (over 1 year ago)
• Last Synced: 2025-03-03T22:31:21.939Z (about 1 year ago)
• Language: Java
• Homepage:
• Size: 20.3 MB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# SReD: Structural Repetition Detector Plugin for ImageJ and Fiji

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SReD (Structural Repetition Detector) is an ImageJ and Fiji plugin for analyzing structural repetition in microscopy images. It introduces a novel approach utilising a custom sampling scheme and correlation metrics to compute Repetition Maps. These maps highlight and quantify the degree of structural repetition present within images, providing valuable insights for image analysis and structural studies.    

| Starter Guide |

|:-:|

| [](https://youtu.be/85coxW4H7f4) |

## Installation

1. Ensure you have ImageJ or Fiji installed on your system. If not, download and install it from:

   - ImageJ: https://imagej.nih.gov/ij/download.html

   - Fiji: https://fiji.sc/

2. Click on "Help > Update... > Manage Update Sites"

3. Click "Add Unlisted Site" and add the SReD update site to the URL box (https://sites.imagej.net/SReD/)

4. Tick the checkbox to include the SReD update site.

5. Click on "Apply Changes" and restart ImageJ/Fiji.

7. The plugin should now appear in the Plugins menu of ImageJ/Fiji under the SReD tab.

## System Requirements

- Java 8 or higher

- OpenCL-capable GPU (recommended for faster processing)

## Usage

After installation, you can access SReD functions from the "Plugins > SReD" menu in ImageJ/Fiji. 

For detailed usage instructions, please refer to the [SReD Wiki](https://github.com/HenriquesLab/SReD/wiki).

## Troubleshooting

If you encounter any issues during installation or usage, please check the [FAQ section](link_to_FAQ) or open an issue on our [GitHub page](https://github.com/HenriquesLab/SReD/issues).

## License

SReD is distributed under the [MIT](LICENSE).

## Citation

If you use SReD in your research, please cite our paper:

[Mendes, A. _et al._ (2024) Structural Repetition Detector: multi-scale quantitative mapping of molecular complexes through microscopy. _Biorxiv_. DOI: 10.1101/2024.09.16.613204

](https://www.biorxiv.org/content/10.1101/2024.09.16.613204v1)