Create synactJ.md

Author: schmiedc

_pages/plugins/synactJ.md

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+---
+title: SynActJ
+icon: https://github.com/schmiedc/SynActJ/blob/master/src/main/resources/LogoSynActJ1.png
+categories: [plugin]
+project: /plugins/Cellular Imaging
+pom-url: https://github.com/schmiedc/SynActJ/blob/master/pom.xml
+---
+
+# 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.
+
+<img src="https://schmiedc.github.io/SynActJ/images/main/teaser.png" alt="Intro" class="inline"/>
+
+## Documentation
+
+Have a look at the github pages site for more information:<br>
+[https://schmiedc.github.io/SynActJ/](https://schmiedc.github.io/SynActJ/)
+<br/>
+<br/>
+
+## 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](https://github.com/schmiedc/SynActJ/blob/master/testInput/testMovie.tif)
+
+The default segmentation parameters should work for this example file.
+
+## Installation
+
+### Image analysis - Fiji plugin
+
+Tutorial for Shiny app: [Link to tutorial](https://schmiedc.github.io/SynActJ/pages/Fiji_Plugin.html)
+
+For the image analysis you need to download and install Fiji: [Link to Fiji](https://fiji.sc/).<br>
+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](https://github.com/schmiedc/SynActJ_Shiny)<br>
+Tutorial for Shiny app: [Link to tutorial](https://schmiedc.github.io/SynActJ/pages/SynActJ_Shiny.html)
+
+For the data analysis you need to download R and RStudio: R Version 4.1.0<br>
+[Link to R](https://cran.r-project.org/bin/windows/base/)<br>
+Select version 4.1.0
+
+RStudio 1.4.1717<br>
+[Link to RStudio](https://www.rstudio.com/products/rstudio/download/)
+
+1. Download the contents of the repository: SynActJ Shiny<br>
+  Click on the green button: **Code**.<br>
+  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.