Fiji Is Just ImageJ

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TrakEM2 is an ImageJ plugin for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation.
TrakEM2 is an ImageJ plugin for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation.


Fiji is an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java3D 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.

Download Fiji now  Yada.png      List of Update sites

How to cite Fiji?      Who is citing Fiji?

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


Subscribe to an RSS or Atom feed of the Fiji news.

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.

Download

We have continuous releases thanks to ImageJ's Jenkins server:

Downloads
Version Arch Win.png Osx.png Tux.png Java.svg Fiji-logo-1.0-128x128.png
Continuous release 32-bit Windows (32-bit) OS X1 Linux (32-bit) N/A All platforms
(no JREs)
64-bit Windows (64-bit) Linux (64-bit)

[1] There is only limited support for PowerPC (G4/G5) Macs, see MacOSX tips for a special download link.

As announced in this mail, we join the legions of construction workers digging up the streets during the second half of July 2013 (i.e. we also use the slow summer month to break things in order to make them better), incorporating extensive changes to reconcile Fiji with ImageJ2. The packages below reflect Fiji as of July 15th, 2013 and are offered here just in case the continuous build (or an updated version) above broke a formerly working operation that is desperately needed, like, right now.
Life-Line version 32-bit Windows (32-bit) OS X1 Linux (32-bit) N/A All platforms
(no JREs)
64-bit Windows (64-bit) Linux (64-bit)


See the Downloads page for debian packages and others.

License

Fiji is released under the General Public License.

Each component has its own license.