Fiji Is Just ImageJ

From Fiji

Fiji is an image processing package. It can be described as a distribution of ImageJ 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  

News

• 2010-08-23 - Neurite Identification Tool for Drosophila brain lineages
• 2010-08-12 - CLAHE speed up
• 2010-08-04 - The Script Editor's font and tab size are now adjustable
• 2010-08-03 - Limited PowerPC Macs support again
• 2010-08-02 - The Retinex plugin is now bundled in Fiji

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The ImageJ conference 2010 is now open for registration:

Browse the news archive.

Documentation

Using Fiji

• What you need to know about scientific image processing
• Installing Fiji
• Getting started with Fiji
• Tutorials
• Find contact information, 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 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.

Transform

• Distortion correction: correct lens deformation induced by the microscope (optical and electron microscopy). See the Distortion Correction plugin manual.

Image registration

• SPIM Registration Registration and fusion of Selective Plane Illumination Microscopy data.
• Stitching 2D/3D Stitch multiple image stacks across X,Y,Z.
• 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
• imglib

Downloads

• Linux
• Linux (64-bit)
• Windows
• Windows (64-bit)
• MacOSX
  Critical: if you update and Fiji does not work anymore, you need to follow these instructions.
  Note: There is only limited support for PowerPC (G4/G5) Macs, see MacOSX tips for a special download link.
• All platforms (includes all JREs)
• All platforms (does not include JREs)

Mirrors:

• University of California, San Francisco, thanks to Nico Stuurman!
• Fiji on GoogleCode (only files smaller than 100MB due to upload restrictions)
• Fiji on SourceForge

See the Downloads page for debian packages and others.

License

Fiji is released under the General Public License.

Each component has its own license.