Difference between revisions of "Fiji"

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;[http://repo.or.cz/w/imageja.git/ ImageJA]
;[http://repo.or.cz/w/imageja.git/ ImageJA]
* The core of Fiji.
* The core of Fiji.
;[[:Category:Skeleton|Skeletons and tree analysis]]
* [[Skeletonize3D|Skeletonize]] and [[AnalyzeSkeleton|Analyze skeletons]]
== [[Downloads]] ==
== [[Downloads]] ==

Revision as of 03:44, 8 September 2009


Fiji is an image processing package based on ImageJ.

For users, Fiji is easy to install and update, bundles a set of plugins in a coherent menu structure (and updatable), along with comprehensive documentation.

For developers, Fiji as an open source project is hosted on a git source 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 Dai.png



Browse the news archive.



TrakEM2: 359 montages of 13x13 tiles of 2048x2048 pixels each.

Stitching of images: Automatically reconstruct tiled 2D/3D acquisitions. The example shown (6 times 512x512x86 px) took 90 seconds.
3D Viewer: hardware-accelerated 3D visualization of image stacks as volumes, orthoslices and meshes.
Simple Neurite Tracer: semi-automatic tracing of neurons.

Feature correspondences: Automatically extracted landmark correspondences using the MOPS descriptor.


3D Viewer
  • Hardware-accelerated 3D volume and mesh visualization, and 3D registration of image stacks.
  • Register/edit/analyze/segment/annotate/3D model terabytes of confocal and electron microscopy images.
Feature Extraction
  • SIFT and MOPS.
Image registration
Stitching 2D/3D
  • Stitch multiple image stacks across X,Y,Z.
VIB Protocol
  • Label-based 3D alignment of image stacks.
  • The core of Fiji.
Skeletons and tree analysis


Update: new version "Dresden-2009" was released.


See the Downloads page for debian packages and others.


Fiji is released under the General Public License.

Each component has its own license.