Both Icy and Fiji are open-source free image analysis softwares based on the Java programming language.
Although they share a lot of similarities, some specificities of Icy are
- its rich graphical user interface, with a customizable ribbon menu giving quick access to key tools and some plugins, a viewer including many visualisation option and an inspector on the side panel allowing to quickly adjust the brightness and contrast and change the LUT of the image, as well as to manage the ROIs. Icy is used quite often for 3D visualisation. For instance, you can have a look at this paper (Fig.2E, Fig.4E-I and supplementary video).
- its graphical programming interface. You can create complex automated image analysis workflows called protocols without prior programming knowledge. Protocols can be hosted on the Icy website and published as part of the material and method of a biology paper. For instance, this protocol was designed for this paper.
- its cutting edge algorithms. Icy was developped and is still maintained in a mathematics lab. It was created as a tool to share the latest image analysis research to biology users.
To get started with Icy, you can have a look at the online training documentation and at the online documentation of each plugin.