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Synaptic Activity in ImageJ (SynActJ)

SynActJ is an image and data analysis workflow that allows to analyze synaptic activity. It is based on a Fiji plugin and a R Shiny App that implement the automated image analysis of active synapses in time-lapse movies. We tested the workflow with movies of pHluorin or calcium sensors.


Documentation & source code

Have a look at the github pages site for more information:

The code is published free and open source under the MIT license.
Please find the source code of the Fiji plugin here:

The source code of the R analysis can be found here:

Core features

  • Java Swing based graphical user interface
  • Interactive adjustment over entire dataset
  • Batch processing executed from main interface
  • Saving and loading of processing settings
  • Shiny App for data processing

Accepted Datasets

Expected are 2D single channel .tif files containing multiple frames. At a specific frame the cultured neurons were stimulated and active boutons show an increase in intensity. The image calibration can be changed in the workflow. A settings file can be provided but can also be created later.

A small example file is provided here: Link to example data

The default segmentation parameters should work for this example file.


Image analysis - Fiji plugin

Tutorial for Shiny app: Link to tutorial

For the image analysis you need to download and install Fiji: Link to Fiji.
The plugin is available via an update site. Add the Cellular-Imaging site:

  1. Select Help › Update… from the menu bar. This will install potential updates and open a new window.
  2. Click on Manage update sites. Which opens the Manage update sites dialog.
  3. Search for the Cellular Imaging update site in the list.
  4. Add the update site by setting the tick box.
  5. Press Close and then Apply changes.
  6. The SynActJ should appear with the Status: Install it.
  7. Press Apply changes wait for download to finish and restart Fiji.

Data analysis - Shiny app

Repository for Shiny app: Link to Repo
Tutorial for Shiny app: Link to tutorial

For the data analysis you need to download R and RStudio: R Version 4.1.0
Link to R
Select version 4.1.0

RStudio 1.4.1717
Link to RStudio

  1. Download the contents of the repository: SynActJ Shiny
    Click on the green button: Code.
    Press Download ZIP to download the scripts.
  2. Unzip the script to a location of your choice.
  3. Open the app.R file in RStudio.
  4. Start the application: press Run App - top right corner of RStudio.
  5. RStudio may ask to install or load extra packages - Download will take some time.
  6. Once these packages are installed and loaded the RShiny GUI should pop up.
  7. Optional: Press Open in Browser for a better rendering of the GUI.