3D image visualization and presentation

We have various tools for visualizing 3D data. This page aims to give you some ideas of what is possible. Sam is happy to help you get started with the software when you have your images.

Stack slider

Before you start, it is a good idea to quickly view the slices in a stack. Most software programs have some simple slider for "moving" up and down the stack viewing one slice at a time like this 4.5 MB GIF animation. This often gives a pretty good impression of the 3D structure and shows if your stack needs croping in any way.

Orthogonal slices

As well as viewing a single XY slice of your dataset, it can sometimes be useful to view the XZ and YZ slices along certain lines of your stack.

Projections

These are pretty much the simplest way of viewing your 3D data as a whole. You can consider a maximum intensity projection (MIP) to be the brightest structures in your 3D z-stack squashed onto a single plane. It is a convenient way of seeing at once all the objects in the different planes of a stack.

Our brains find it quite helpful for better appreciating the depth of an object to see a rotation - a series of MIPs made at different angles. . .

HOWTO: Make projections in Zeiss confocal sofware

You can also make projections in the Leica LAS software, ImageJ, MetaMorph and Huygens. Volocity offers advanced controls for 3D visualization and allows the export of very visually impressive movie sequences.

Surface render

Volumes can be visualized by generating an isosurface, a 3D threshold where all the points on the surface have the same intensity. This approach tends to be useful when you are trying to represent the overall structure of an object or relatively distinct objects within your stack.