Wednesday, January 23, 2008

Managing 3D Data

Many folks out there in the paleo community are starting to use three dimensional data in some form or another. So, what free or open source options are out there? This post introduces a few of the major programs. Over the next few months (and probably between other posts), I plan on reviewing each piece of software in more detail. But, here's a quick review of some of the "shining stars" out there in the open source world. These are the programs that I *always* have on my computer.

The classic scientific image manipulation program. This program is free, fast, and flexible, and it will do a variety of tasks (automatic counting, generation of AVI files from stacks of images, DICOM viewing, simple reslicing and 3D rendering, calibrated measurements, to name a few), many of them quite well. A robust and active plugin library, along with cross-platform compatibility (ImageJ runs in Java), make this a "must have" for anyone dealing with images.

3D Slicer

If you ever want to generate three dimensional surface reconstructions from CT scan data, look no further. 3D Slicer is powerful, relatively fast, and in very active development (the beta for version 3.0 was just released). Use it to make 3D renderings, measure volumes, or segment data for analysis in other programs.

MIPAV, another Java-based image manipulation program, picks up where ImageJ left off. MIPAV's big strength is the ease with which it manipulates large stacks of images, and its easy export to pretty much any medical imaging format.


This program is fantastic for manipulating or rendering those surface models that you generate in Slicer. ParaView also is capable of doing renderings of other forms of data, such as FEM results, volume renderings from CT data, etc. This is another very active and useful open source program.


Matt BK said...

Do you know of any open-source or free software for doing 3d plots of PCA scores? I have not been able to locate any.

Andy said...

For R, there are a few options. One I found is at here (but I haven't used this function before, so I don't know how well it works. . .)

A number of programs out there will plot points in 3D - I haven't done much of this, so I can't make a specific recommendation. Some examples are found at:

Free Statistical Software

A program called "ViSta" will also plot 3D charts, as well as perform PCA. . .haven't used it in forever though, so I'm not much help beyond that. This is probably the most "user friendly" of the options I've mentioned here, though.

Nick said...

Is there a way to save models in 3D Slicer as STLs?