Revision as of 11:04, 5 December 2009 by Schindelin (talk | contribs) (update to the latest version)

TrakEM2 (ImageJ)
Author Albert Cardona
Maintainer Albert Cardona (
File TrakEM2_.jar (Included in Fiji)
Source trakem2 git repository
Initial release May 2006
Latest version 0.7m (4 December 2009)
Development status active
Category Registration, Segmentation, Image annotation, Plugins
Website TrakEM2 news and documentation

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

See TrakEM2 snapshots for an overview.


  • Segmentation: manually draw areas across stacks, and sketch structures with balls and pipes.
  • Measurements: volumes, surfaces, lengths, and also measurements via ImageJ ROIs.
  • Image Registration: register floating image tiles to each other using SIFT and global optimization algorithms.
  • 3D Visualization: interacting with the 3D Viewer plugin, TrakEM2 displays image volumes and 3D meshes of all kinds.
  • Image Annotation: floating text labels.
  • Semantic segmentation: order segmentations in tree hierarchies, whose template is exportable for reuse in other, comparable projects.

TrakEM2 interacts with the 3D Viewer for visualization of image volumes and 3D meshes.

TrakEM2 in Fiji

  • Create new projects from "File - New - TrakEM2 (blank)"
  • Open an existing project by dragging its .xml file onto the toolbar, or via "File - Open".



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

TrakEM2 Display showing 9 images in a layer, where 2 images and one floating text label (set to 30% transparency) are selected (pink and white frames; white is the active one – note the corresponding pink and blue coloration of the object panels on the left). The Navigator (bottom left) paints a red frame to indicate the area currently displayed in the canvas (right).
3D Viewer: hardware-accelerated 3D visualization of image stacks as volumes, orthoslices and meshes. Above, secondary lineages of Drosophila third instar larval brain segmented in TrakEM2.
The three TrakEM2 trees, as an interface for editing and visualizing the three internal TrakEM2 data structures.

Example TrakEM2 segmentations, including Ball, Pipe, Profile, AreaList and floating text labels.