A graphical user interface for Fiji that provides access to a curated suite of fluorescence image visualization and processing tools commonly needed by life scientists.
Please consult the wiki page.
EasyFiji has been tested on Mac, Linux and Windows to ensure cross-platform compatibility.
Software dependencies can be found in pom.xml
This Fiji GUI plugin is developed using the SciJava framework and follows the ImageJ plugin architecture.
| Component | Version / Notes |
|---|---|
| Java JDK | JavaSE-1.8 (Java 8) |
| Maven | 3.9.9 |
| IDE | VScode (1.104.2) |
| Build Tool | Maven (builds .jar under /target) |
| ImageJ | 1.54p |
Developers can easily extend it by adding new panels, button listeners, or processing classes following the same event-driven design pattern. after modify, type "mvn clean install" to generate new .jar file. The compiled .jar file will appear in target folder.
Make sure EasyFiji_2-..*.jar is insdie the plugins folder of Fiji and restart.
Images must be opened and selected (active window).
Long-running process (e.g., filters, intensity correction, large image files) could run slow, any interactiion with the images and fiji commands (change channel, adjusting contrast, ...) could potentially interrupt the process causing Fiji freeze. Restart Fiji can help!
Duo to Fiji internal bugs, sometimes the image won't auto updates when clicking apply luts under Process Tab. The image pixel value are actually modified (function works!) and switch color channel can see fix the display issue.
Some buttons (color fusion and ) call the macro scripts (reside in resources/scripts/) to perform the functions, people can also use these scripts directly without EasyFiji. More custom scripts can be easily further added to extend the community usability.
EasyFiji use features that that are bundled with newer version of Fiji like Kymograph and BioFormats, Please install these plugins if want to use these features.
If you encounter a bug, installation problem, or unexpected behavior, please create a issue through the project's GitHub page. (please include operating system, fiji version, steps to reproduce the error, possible example image, error messages, screenshots if available)
Released under the Apache License 2.0. See LICENSE file for details.