While ImageJ with its plugins could handle most of the 2D image analysis and processing, there is really no good free-of-charge way to handle 3D images. Until now, http://penglab.janelia.org/proj/v3d/.
My quick test was not very impressing ...
Almost any software handles 3D could display surface view, change LUT, rotate, record movies, ... etc. But, remember V3D is free! Other commercial ones cost a lot $ $ $ $
Until the moment I tried a right click on an objective - direct 3D pinpoint function of V3D. What's this pinpoint function? Basically it is how you can select an objective in 3D. The method using two right-click to define one objective is "plain" and slow ~~ The method using one right-click and the mean-shift algorithm scanning over the center of mass of the projection ray to estimate the 3D location really WOW me!
As you can see from the image above, the objectives were identified pretty accurately in 3D - of course, you may say that these are nucleus and easy to identify.
Other cool features like easy handling over gigabyte data, automatic segmentation, neuron tracing ... If you are working with 3D images, give it a try. It may not be your final first-choice 3D image analysis tool due to various reasons. But it will definitely re-open your eyes on how to handle 3D images. By the way, there is a toolbox of V3D for linking to matlab.
Related publication
V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets
Hanchuan Peng, Zongcai Ruan, Fuhui Long, Julie H Simpson & Eugene W Myers
Nature Biotechnology (2010) DOI: 10.1038/nbt.1612
Received 30 November 2009
Accepted 08 February 2010
Published online 14 March 2010The V3D system provides three-dimensional (3D) visualization of gigabyte-sized microscopy image stacks in real time on current laptops and desktops. V3D streamlines the online analysis, measurement and proofreading of complicated image patterns by combining ergonomic functions for selecting a location in an image directly in 3D space and for displaying biological measurements, such as from fluorescent probes, using the overlaid surface objects. V3D runs on all major computer platforms and can be enhanced by software plug-ins to address specific biological problems. To demonstrate this extensibility, we built a V3D-based application, V3D-Neuron, to reconstruct complex 3D neuronal structures from high-resolution brain images. V3D-Neuron can precisely digitize the morphology of a single neuron in a fruitfly brain in minutes, with about a 17-fold improvement in reliability and tenfold savings in time compared with other neuron reconstruction tools. Using V3D-Neuron, we demonstrate the feasibility of building a 3D digital atlas of neurite tracts in the fruitfly brain.
just came back from Imaris demo by Matt
I would say that, if you get the funding, definitely go Imaris - it is much powerful and user friendly than V3D, of course, very expensive
it's said V3D also support plugins. haven't try that yet
I tried once and didn't work out.
I am a user and I just want it work.
By the way, there is very limited number of plugins at this moment ...