A 3D editing plugin


This is a 3D modelling plugin for ImageJ, and has been designed with confocal stacks of images in mind, but works with any stack.

A stack represents a volume. It is assumed the user knows the depth, that is, the distance in pixels between any two consecutive slices of the stack.

How it works: the user outlines a structure on as many slices as such structure appears. A group of curves (=outlines) defines an object.

This group of 2D curves is used to generate a skin (a 3D object), which is saved in .dxf format. It can be opened in applications such as Blender (free opensource application available at blender.org), AutoCAD, Maya and Amira.

The user can make as many objects as needed in the same stack, by assigning different group names to every object.

The plugin offers 6 different tools for outlining structures, which can not be mixed for a given object: i.e. a given object has to be outlined in full using the same tool. Different objects in the same stack can be outlined using different tools.

6 Tools for outlining

  • Bezier tool: bezier curves (if you are familiar with Adobe Illustrator paths, it's about the same). The user clicks and drags on the screen to set points and interpolation points. Only closed curves are suitable for skin making.
  • Brush tool: the user defines the radius of the brush and paints the area to be outlined.
  • Wand tool: uses ImageJ wand. Works in 8-bit images only.
  • Ball tool: every click sets a circle with a user-defined radius. That circle will be present as a sphere in the 3D model.
  • Pipe tool: uses open bezier curves. Every click sets a joint of the pipe, with a user-defined radius.
  • BSpline tool: uses spline interpolation method. Clicked points are not on the curve, which can make outlining difficult.


  • Turn any curve into a polygon or polyline ROI. This allows for image editing -painting, erasing, copying- and also measuring.
  • Works with magnification: use ImageJ glass and hand tool to magnify and navigate the image.
  • Supergrouping: outline a structure as several objects but join them a single object in the DXF file.
  • Measure volume of each outlined structure (in cubic pixels and cubic micrometers).
  • Draw outlined curves in a new, black-filled stack.
  • Clone curves between slices, displacing each copy through X and Y.
  • Copy curves between slices.
  • Modify saved curves. Useful to model structures that present an increasingly visible area at every stack slice.
  • Save curves to be opened in other sessions. Also, it's a very compact method to store 3D data.
  • Undo: all steps can be undone at any point. The user can define the amount of saved steps in the 'Options' dialog.