Paredes-GrillSpectorLabs Fiji/ImageJ Update Site

This repository contains a collection of several ImageJ scripts that process and analyze tile scan microscope images.

Installation

To access our plugins directly from your Fiji/ImageJ download, follow our update site using our the URL https://sites.imagej.net/Paredes-GrillSpectorLabs/.

Development

This repository uses Maven for versioning and building jar files. To further develop our code

1. Clone this repository using git clone https://github.com/VPNL/FijiUpdateSite.git.
2. Edit and add Fiji plugin scripts under FijiPyPlugins/src/main/resources/scripts/Plugins. You can use or further develop our Python helper functions and object classes under FijiUpdateSite/FijiPyLib/src/main/resources. Additionally, we have some Matlab functions saved under MatScripts that can be used or edited for image processing steps.
3. Edit pom.xml files to reflect your project information.
4. Run mvn -Dscijava.app.directory=/path/to/your/ImageJ.app to build jar files with your code and copy them directly into your ImageJ/Fiji installation.