ImageJ:Featured Projects

  • TrakEM2|TrakEM2-snapshot.jpg

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

  • 3D Viewer|3D-Viewer-snapshot.jpg

The hardware-accelerated 3D Viewer uses Java3D to display surfaces, orthogonal slices and to perform volume rendering.

  • Simple Neurite Tracer|SimpleNeuriteTracer-snapshot.jpg

The Simple Neurite Tracer allows you to segment linear structures in 3D images by marking both ends in 3D and letting the tracer work out the rest.

  • Stitching|Stitching-snapshot.jpg

The Stitching plugin makes it a breeze to stitch multiple overlapping recordings of a single specimen into a single 3D image.

  • Feature Extraction|FeatureExtraction-snapshot.jpg

The Feature Extraction plugins provide fully automatic detection of SIFT or MOPS features and registration using corresponding features of two images.

  • Update Fiji|Updater-snapshot.jpg

Stay up-to-date with the Fiji Updater.

  • 3D Viewer|3D_Viewer-snapshot.jpg

The 3D Viewer plugin can display 3D stacks via volume rendering, isosurfaces or as orthoslices.

  • TrakEM2|TrakEM2-snapshot-2.jpg

The TrakEM2 plugin can be used to annotate images non-destructively.

  • TrakEM2|TrakEM2-snapshot-3.jpg

The TrakEM2 plugin offers a range of manual and semi-automatic segmentation tools.

  • SIOX|SIOX-snapshot.jpg

The SIOX plugin provides semi-automatic segmentation of color images via Simple Interactive Object Extraction.

  • SPIM Registration|SPIM Registration-snapshot.jpg

The SPIM Registration plugin provides fast, reliable and high-precision registration and fusion of Selective Plane Illumination Microscopy data as well as other 3d multi-angle image acquisitions.

  • TrakEM2|TrakEM2 neuronal reconstruction-snapshot.png

The TrakEM2 plugin provides the means to reconstruct neuronal arbors in 3D, including relationships between trees to represent synapses.

  • TrakEM2|TrakEM2-display-2-snapshot.png

The TrakEM2 provides the means to manually reconstruct neurons and synapses with 3D arbors and connector objects that relate them.