* '''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.