Fiji Is Just ImageJ

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The TrakEM2 plugin provides the means to [http://www.ini.uzh.ch/~acardona/trakem2_manual.html#trees reconstruct neuronal arbors in 3D], including [http://www.ini.uzh.ch/~acardona/trakem2_manual.html#connectors relationships between trees] to represent synapses.
The TrakEM2 plugin provides the means to reconstruct neuronal arbors in 3D, including relationships between trees to represent synapses.


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 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:

Ij2-logo.jpg Bio-formats.png Ome-logo.png Mm-logo.jpg Knime-logo.jpg
ImageJ2 Bio-Formats OME µManager KNIME

News


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Browse the news archive.

Documentation

Using Fiji

Advanced Fiji usage

Developing for Fiji

Projects

3D Viewer
  • Hardware-accelerated 3D volume and mesh visualization, and 3D registration of image stacks.
Transform
Image registration
Segmentation
Tracking
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.

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.

Template:DownloadsCurrent

See the Downloads page for debian packages and others.

License

Fiji is released under the General Public License.

Each component has its own license.