Fiji Is Just ImageJ Tweet

Call for papers for the ImageJ user & developer conference 2012!

The TrakEM2 plugin offers a range of manual and semi-automatic segmentation tools.

Fiji is an image processing package. It can be described as a distribution of ImageJ (and soon ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.

The main focus of Fiji is to assist research in life sciences.

For users, Fiji is easy to install and has an automatic update function, bundles a lot of plugins and offers comprehensive documentation.

For developers, Fiji is an open source project hosted in a Git version control repository, with access to the source code of all internals, libraries and plugins, and eases the development and scripting of plugins.

Download Fiji now  

How to cite Fiji?

Collaboration

The Fiji project is driven by a strong desire to improve the tools available for life sciences to process and analyze data. To this end, Fiji collaborates closely with the following projects:

ImageJ2	Bio-Formats	OME	µManager	KNIME

News

• 2013-05-14 - Trainable Segmentation refactoring
• 2013-05-10 - Fiji Archipelago Cluster Beta
• 2013-05-03 - SPIMage processing recipes for a cluster
• 2013-02-25 - TrackMate v2.0.0 released
• 2013-02-09 - OpenSPIM wiki goes public

Subscribe to an RSS or Atom feed of the Fiji news.

Browse the news archive.

Documentation

Using Fiji

• What you need to know about scientific image processing
• Installing Fiji
• Getting started with Fiji
• Tutorials (also external ones)
• Find contact information (also how to get an account on this Wiki), mailing list, IRC (chat) and help
• Frequently Asked Questions
• more...

Advanced Fiji usage

• Registering 3D images
• Segmenting images
• Useful keyboard shortcuts
• Scripting: with Macros, in Beanshell, in Javascript, in JRuby, in Jython, in Clojure (see also Scripting Help).
• Some ImageJ tricks
• Links
• more...

Developing Fiji

• Overview of Fiji's source code
• Compile Fiji from source code
• more...

Projects

3D Viewer

• Hardware-accelerated 3D volume and mesh visualization, and 3D registration of image stacks.

TrakEM2

• Register/edit/analyze/segment/annotate/3D model terabytes of confocal and electron microscopy images.

ImgLib2

• Generic and extensible n-dimensional image processing library for Java.

Transform

• Interactive image transformation (rigid, similarity, affine, perspective, deform)
• Interactive Stack Rotation
• Landmark based transformation and deformation
• Panorama Viewer
• Distortion correction: correct lens deformation induced by the microscope (optical and electron microscopy). See the Distortion Correction plugin manual.

Image registration

• Elastic Alignment and Montage
• SPIM Registration Registration and fusion of Selective Plane Illumination Microscopy data.
• Image Stitching Stitch multiple image stacks across X,Y,Z,T and C.
• Feature Extraction SIFT and MOPS.
• Consistent and elastic 2D registration (bUnwarpJ)
• Stack slice registration
• Image montage (via TrakEM2) with global optimization (in 2D and across sections)
• VIB Protocol Label-based 3D alignment of image stacks.

Segmentation

• Simple Neurite Tracer (project page)
• Segmentation Editor
• Manual (via TrakEM2)
• Level Sets
• Trainable Segmentation
• SIOX: Simple Interactive Object Extraction

Analysis

• Skeletons and tree analysis

The core of Fiji.

• ImageJA

Downloads

Critical: if you updated and Fiji does not work anymore, you need to follow these instructions.

Download

We have continuous releases thanks to ImageJ's Jenkins server:

Downloads
Version	Arch
Continuous release	32-bit	Windows (32-bit)	OS X1	Linux (32-bit)	N/A	All platforms (no JREs)
	64-bit	Windows (64-bit)		Linux (64-bit)

[1] There is only limited support for PowerPC (G4/G5) Macs, see MacOSX tips for a special download link.

See the Downloads page for debian packages and others.

License

Fiji is released under the General Public License.

Each component has its own license.