https://github.com/joda01/evanalyzer

EVAnalyzer 1 - EV analyzing plugin for Fiji
https://github.com/joda01/evanalyzer

bioinformatics biology ev fiji-plugin imagej-plugins

Last synced: 5 months ago
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EVAnalyzer 1 - EV analyzing plugin for Fiji

• Host: GitHub
• URL: https://github.com/joda01/evanalyzer
• Owner: joda01
• License: gpl-3.0
• Created: 2020-09-26T19:53:21.000Z (over 5 years ago)
• Default Branch: main
• Last Pushed: 2025-06-03T20:26:48.000Z (about 1 year ago)
• Last Synced: 2025-06-04T05:13:42.116Z (about 1 year ago)
• Topics: bioinformatics, biology, ev, fiji-plugin, imagej-plugins
• Language: Java
• Homepage:
• Size: 317 MB
• Stars: 4
• Watchers: 1
• Forks: 0
• Open Issues: 6
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
[![Release to Update Site](https://github.com/joda01/evanalyzer/actions/workflows/release.yaml/badge.svg)](https://github.com/joda01/evanalyzer/actions/workflows/release.yaml)

# EVAnalyzer

Please forward to [EVAnalyzer 2](https://github.com/joda01/imagec) powered by ImageC

![./doc/screenshot_v80.png](./doc/screenshot_v80.png)

[](https://onlinelibrary.wiley.com/doi/full/10.1002/jev2.12282)

## Description

EVAnalyzer is a Fiji ImageJ plugin designed for analyzing microscope pictures of EVs. This plugin can be used for:

*  Counting the number of EVs.

*  Calculating the colocalization of evs and other particles.

*  Detect biological cells and counting EVs updatekn from cells.

*  Analysis of a large amount of images automatically.

*  Generating XLSX (Excel) reports with automatic statistics generation.

## Installation

*  Download and instal Fiji from [Fiji](https://imagej.net/Fiji/Downloads).

*  Add EVAnalyzer to update sites:

  1.  Open Fiji

  2.  Click `Help -> Update`

  ![add_update_site_01.png](doc/add_update_site_01.png)

  3.  Click `Manage update sites`

  ![add_update_site_02.png](doc/add_update_site_02.png)

  4.  Click `Add update site`

    ![add_update_site_03.png](doc/add_update_site_03.png)

  5. Look `EVAnalayzer` in the update site list or enter `EVAnalayzer` in name field and `https://sites.imagej.net/evanalyzer/` in the URL field

    ![add_update_site_04.png](doc/add_update_site_04.png)

  6. Restart Fiji

## Roadmap

- [ ] Make it possible to automatically generate reports for 10'000 and more images per run.

- [ ] Export of `R` files and automatic diagram generation.

- [ ] Implement automatic unit test as positive and negative control reference to be sure that an update does not influence future analysis results.

- [ ] Improve preview functionaltity to be more detailed.

- [ ] Extend to support more than 5 channels.

- [ ] Include handbook and Help functionality directly from the PlugIn.

## Contributing

If you have some questions, feature requests or if you found a bug, please just create an issue in the Issues tab.

## Coding

For development Visual Studio Code is used. Compiling is done within a docker image (dev container).

*  Download and install [Visual Studio Code](https://code.visualstudio.com/)

*  Install ```Remote Container``` plugin.

*  Clone the repository and open the cloned folder in Visual Studio Code.

*  Reopen the project in Dev Container.

*  Run ```./build.sh``` to compile the project.

## Common issues

*  Images used in the plugin cannot be in the RGB format, and must be monochromatic.

*  Actually VSI, TIFF, ICS, and CZI images can be processed.

---

## Research Article

First published: 27. November 2022 | https://doi.org/10.1002/jev2.12282

## Cite

Schürz, M., Danmayr, J., Jaritsch, M., Klinglmayr, E., Benirschke, H. M., Matea, C. -. T., Zimmerebner, P., Rauter, J., Wolf, M., Gomes, F. G., Kratochvil, Z., Heger, Z., Miller, A., Heuser, T., Stanojlovic, V., Kiefer, J., Plank, T., Johnson, L., Himly, M., … Meisner-Kober, N. (2022). EVAnalyzer: High content imaging for rigorous characterisation of single extracellular vesicles using standard laboratory equipment and a new open-source ImageJ/Fiji plugin. Journal of Extracellular Vesicles, 11, e12282. https://doi.org/10.1002/jev2.12282