Difference between revisions of "Fiji"

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* [[Plugins_Menu#Segmentation|Level Sets]].
* [[Plugins_Menu#Segmentation|Level Sets]].
* [[Distortion correction]]: see the [http://www.kaynig.de/downloads/DistortionCorrectionPlugin_Manual.pdf Distortion Correction plugin manual].
* [[Distortion correction]]: correct lens deformation induced by the microscope (optical and electron microscopy). See the [http://www.kaynig.de/downloads/DistortionCorrectionPlugin_Manual.pdf Distortion Correction plugin manual].
;[[VIB Protocol]]
;[[VIB Protocol]]
* Label-based 3D alignment of image stacks.
* Label-based 3D alignment of image stacks.

Revision as of 09:26, 24 October 2008


Fiji Is Just ImageJ (batteries included)



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.


Update: the MacOSX version crashed on most Macs; the link below points to a fixed version.

See the Downloads page for debian packages and others.


Fiji is released under the General Public License.

Each component has its own license.