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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.
See a lot more snapshots
TrakEM2 video tutorials
Example data sets
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
TrakEM2 video tutorials
2012-07-04 - 1.0a released
Milestone release: 1.0a. TrakEM2 is now feature complete.
- New contextual menu items "Patch - Open image" and "Patch - Open original image".
- Create subproject can ignore hidden images.
- Fix bug #351, related to exporting flat images without mipmaps.
- Fix error in removing Stack ZDisplayable instances.
- Fix error in "Save as", didn't allow for ".xml.gz" extension.
- Fix error in duplicating Patch.
- Fix for long-standing error in the form of lack of undo upon clicking and dragging a tile very slightly.
- Layer alignment and montaging dialogs are split into multiple consecutive dialogs.
- Removed "Integral area averaging" as a possible mode for mipmaps, makes no sense anymore and "Area averaging" is better and faster.
- Coping with changes in the ImageJ API regarding ByteProcessor.setMinAndMax, which is no longer destructive.
- Some speed-ups by using the API better.
- New filters NormalizeLocalContrast (sort of like CLAHE but accelerated with integral images), DefaultMinAndMax, ResetMinAndMax and EnhanceContrast.
- Deal with potentially null FileInfo, adapting to changes in the ImageJ ij.jar library.
- "Prepaint" display property is disabled by default. Does no longer make much sense to have it.
- Long list of big and small fixes. See the git log.
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.
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Download and Install
For a manual installation:
See the TrakEM2 Installation How-To
for all details and required additional files
What can you do with it?
- Semantic segmentation editor: order segmentations in tree hierarchies, whose template is exportable for reuse in other, comparable projects.
- Model, visualize and export 3D.
- Work from your laptop on your huge, remote image storage.
- Work with an endless number of images, limited only by the hard drive capacity. Dozens of formats supported thanks to LOCI Bioformats and ImageJ.
- Import stacks and even entire grids (montages) of images, automatically stitch them together and homogenize their histograms for best montaging quality.