Fiji Is Just ImageJ
|The 3D Viewer plugin can display 3D stacks via volume rendering, isosurfaces or as orthoslices.|
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 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.
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:
- 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
Browse the news archive.
- 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
Advanced Fiji usage
- Registering 3D images
- Segmenting images
- Useful keyboard shortcuts
- Some ImageJ tricks
- Hardware-accelerated 3D volume and mesh visualization, and 3D registration of image stacks.
- 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.
- 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.
- Simple Neurite Tracer (project page)
- Segmentation Editor
- Manual (via TrakEM2)
- Level Sets
- Trainable Segmentation
- SIOX: Simple Interactive Object Extraction
- Generic and extensible n-dimensional image processing library for Java.
- Register/edit/analyze/segment/annotate/3D model terabytes of confocal and electron microscopy images.
- The core of Fiji.
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.
We have continuous releases thanks to ImageJ's Jenkins server:
|Continuous release||32-bit||Windows (32-bit)||OS X1||Linux (32-bit)||N/A||All platforms|
|64-bit||Windows (64-bit)||Linux (64-bit)|
 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.
Fiji is released under the General Public License.
Each component has its own license.