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Fiji is an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java3D 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.

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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:

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ImageJ2	Bio-Formats	OME	µManager	KNIME

News

• 2018-03-16 - Classifying microscope image focus quality with deep learning
• 2018-01-11 - Announcing the new Scientific Community Image Forum
• 2017-12-29 - ImageJ2 and Fiji updated - now with search bar!
• 2017-12-04 - Fiji + KNIP hackathon
• 2017-11-29 - ImageJ2 paper published in BMC Bioinformatics

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Browse the news archive.

Documentation

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Projects

3D Viewer

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

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

Tracking

• TrackMate

Analysis

• Skeletons and tree analysis

ImgLib2

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

TrakEM2

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

The core of Fiji.

• ImageJA

Downloads

Critical: if your updater does not work any longer, please drag & drop this link to your Fiji main window and follow the instructions in the text window. If that does not work, pleasefollow these instructions.

See the Downloads page for debian packages and others.

License

Fiji is released under the General Public License.

Each component has its own license.

Fiji is an Open Source project, so everybody is welcome to contribute with plugins, patches, bug reports, tutorials, documentation, and artwork. If you'd like to share any idea or project with us, please contact us via the mailing list or via IRC.

Support

Fiji is supported by several laboratories and institutions:

• LOCI in Madison, Wisconsin, USA, home of ImageJ2 and Bio-Formats.
• The Tomancak Laboratory in Dresden, Germany.