ImageJ

In a joint project, we work towards using ImageJ in the context of neuroanatomy. The people involved are:

AmiraMesh Reader / Writer

In the Würzburg group, we work a lot with Amira, and we work a lot with ImageJ.

To make the work easier, we wrote plugins to read and write 3d stacks in the Amira Mesh format in ImageJ.

Amira Surface Viewer

Amira can write 3d surface files. These can be loaded and visualized in ImageJ with the ShowAmiraSurface plugin.

ROI Brush

Tom Larkworthy wrote the ROI Brush, a tool which does not paint, but instead (un)selects circular regions.

Delaunay / Voronoi diagram

Gabriel Landini had this on his wishlist...

Two Point Correlation

This plugin plots a correlation / distance graph. It was requested by Paul Stutzman, but I have not heard back from him.

Scrollable StackWindow

With this plugin, you can select the current slice with your mouse wheel.

Align Image

Use this plugin to align an image to a template image, by selecting a line in both images.

Moving Least Squares

Warp an image using a technique presented by Schaefer et al. in Image Deformation Using Moving Least Squares.

IsoSurface Extractor

This plugin makes an isosurface from an image stack. It displays the result in a 3d window (you can zoom, pan and rotate the surface), and optionally saves the result as a VRML.

3D Viewer

This plugin offers 3D visualisation of image stacks. This covers texture based volume rendering as well as surface extraction and visualisation.