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What is it?

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


Four movies:

See a lot more snapshots and movies.

TrakEM2 video tutorials for users.

Example data sets

Latest news

Download latest Fiji with TrakEM2 or go to menu "Help - Update Fiji".
Pull source code from the git repos.
Stay up to date with Fiji.
TrakEM2 class diagram for programmers.
TrakEM2 video tutorials for users.

2012-07-04 - 1.0a released

Milestone release: 1.0a. TrakEM2 is now feature complete.

Thanks to Stephan Saalfeld for the final touches to his image registration library and graphical interface!

2011-04-12 - Open Connectome Project hosts an ssTEM image data set online with CATMAID

The Open Connectome Project is hosting an ssTEM image data set of 1200 serial sections from Bock et al. (Nature 2011). The data was analyzed with TrakEM2, using the Treeline and Connector data types to reconstruct neuronal arborizations and their synapses of the mouse visual cortex.

The image data set is deployed online with CATMAID, the Collaborative Annotation Toolkit for Massive Amouts of Image Data. TrakEM2 is able to export its image data set to CATMAID with "Export - Flat Image" (with "For web"), and Treeline, AreaTree and Connector instances are currently exported with custom scripts.

Read all news here.

Download and Install

Managed installation:
For a manual installation:
See the TrakEM2 Installation How-To for all details and required additional files.

What can you do with it?