Revision as of 04:11, 16 October 2008 by Albertcardona (talk | contribs)
TrakEM2 (ImageJ)
Author Albert Cardona
File TrakEM2_.jar
Source [1]
Initial release May 2006
Latest version 25 August 2008
Development status active
Category Category:Registration, Category:Segmentation, Category:Annotation
Website [2]

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