Difference between revisions of "TrakEM2"

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|style="vertical-align:top" |[[Image:Trakem2-snap.jpg|thumb|240px|TrakEM2: 359 montages of 13x13 tiles of 2048x2048 pixels each.]]
 
|style="vertical-align:top" |[[Image:Trakem2-snap.jpg|thumb|240px|TrakEM2: 359 montages of 13x13 tiles of 2048x2048 pixels each.]]
 
|style="vertical-align:top" |[[Image:3D-Viewer.jpg|thumb|240px|3D Viewer: hardware-accelerated 3D visualization of image stacks as volumes, orthoslices and meshes. Above, secondary lineages of <i>Drosophila</i> third instar larval brain segmented in TrakEM2.]]
 
|style="vertical-align:top" |[[Image:3D-Viewer.jpg|thumb|240px|3D Viewer: hardware-accelerated 3D visualization of image stacks as volumes, orthoslices and meshes. Above, secondary lineages of <i>Drosophila</i> third instar larval brain segmented in TrakEM2.]]
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|style="vertical-align:top" |[[Image:TrakEM2-trees.png|thumb|240px|The three TrakEM2 trees, as an interface for editing and visualizing the three internal TrakEM2 data structures.]]
 
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Revision as of 04:39, 16 October 2008

TrakEM2 (ImageJ)
Author Albert Cardona
Maintainer
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.

Features

  • 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.

Documentation

Examples

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.
The three TrakEM2 trees, as an interface for editing and visualizing the three internal TrakEM2 data structures.