BIOP / EasyXT-FIJI

Commands and Classes for interfacing between Imaris and Fiji

EasyXT for ImageJ

An Imaris Xtension for ImageJ.

This collection of Java-friendly APIs can help simplify the interaction between ImageJ and Imaris when writing XTensions.

Installation for End Users

In Fiji

To install EasyXT, you need to add and activate the following update sites in Fiji :

• PTBIOP : https://biop.epfl.ch/Fiji-Update/
• 3D ImageJ Suite :https://sites.imagej.net/Tboudier/

In Imaris

1. Under File > Preferences > Custom Tools make sure to set the Fiji folder
2. Open an image
3. Use Fiji>Image To Fiji which will make Imaris copy the necessary propietary JARs into your Fiji Installation

To Test

1. Open a small dataset in Imaris
2. Open Fiji
3. Go to Plugins>BIOP>EasyXT>Get Complete Imaris Dataset
4. You should have our dataset in Fiji Now

For Developers

Requirements : Imaris version above 9.5.1

To work on the repository :

1. Have Imaris installed
2. Clone the repository
3. Run Imaris
4. Ready to go ! - You can run the EasyXT Main method

JavaDoc

There is an as-complete-as-possible JavaDoc available at https://biop.github.io/EasyXT-FIJI/javadoc/apidocs/

Examples

You will find example code in the ch/epfl/biop/imaris/demo folder

Roadmap

Currently, we are working on getting the API to work and stabilize, before creating ImageJ Commands that can be macro-recorded. This project is mainly intended to be used as an API when writing Groovy scripts.