EasyFiji: A Graphical Interface for User-Friendly Fluorescence Image Processing in Fiji

Fiji (Fiji Is Just ImageJ) is an extensive and extensible open-source image processing package widely employed by the bioimage analysis community. However, for non-computational life scientists, manually interacting with Fiji's many capabilities requires learning and navigating a deeply layered menu system. Moreover, some commands' default behaviors are non-ideal for fluorescence image display and processing. To increase efficiency for life scientists working with fluorescence microscopy images, we have developed EasyFiji, a curated graphical user interface (GUI) plugin for Fiji. Each EasyFiji command is executed via tooltip-enhanced buttons and sliders and always exhibits channel-specific execution, as required for fluorescence images. Commands that alter pixel intensities are also single-click undoable to enable more interactive processing and can be automatically recorded and saved as text for record keeping. An image info panel displays settings crucial for image interpretation. New image rendering and bleach correction functions are also provided. The plugin is freely available on GitHub and as a Fiji Update Site. This protocol outlines the steps to use EasyFiji's interface for visualization and processing of fluorescence microscopy images.