Fiji Is Just ImageJ

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The TrakEM2 provides the means to manually reconstruct neurons and synapses with [ 3D arbors] and [ connector] objects that relate them.
The TrakEM2 provides the means to manually reconstruct neurons and synapses with 3D arbors and connector objects that relate them.

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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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:

55px Bio-formats-icon.png Ome-logo.png Mm-icon.jpg Knime-logo.jpg
ImageJ2 Bio-Formats OME µManager KNIME


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


See the Downloads page for debian packages and others.


Fiji is released under the General Public License.

Each component has its own license.