3D Image Viewer

Posted by Jiro Doke, April 5, 2013

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Note

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Jiro's pick this week is Imagine by Christian Wuerslin.

This is just a cool app. It's a 3D image viewer with a well-designed user interface. I'm sure this will be useful to anyone working with slices of 3D images.

clear
load data
whos

  Name      Size               Bytes  Class    Attributes

  D         4-D               442368  uint8              
  S         4-D             21327411  uint8

Both "D" and "S" (pardon the nondescript names) are volumes of MRI data. "D" is from a data set that ships with MATLAB (load mri).

fprintf('Size of D:   %d x %d x %d x %d\n', size(D));

Size of D:   128 x 128 x 1 x 27

I created "S" from BrainWeb: Simulated Brain Database. They have simulated MRI data that people can use to test imaging techniques. I downloaded the "normal brain" data and the "MS lesion brain" data. I combined the two 3D MRI data, along with the difference between the two data sets, into a single variable "S".

fprintf('Size of S:   %d x %d x %d x %d\n', size(S));

Size of S:   181 x 217 x 181 x 3

Here's a peek at what this app can do. A few points to note:

If you load in a 3D data set, you can scroll through the different slices using the scroll wheel on your mouse. You can also rotate to a different angle.
The 4th dimension is displayed in different panels, and the data sets can be explored in sync.
You can create custom analyses for a line profile or a polygon ROI. The tool comes with a default analysis routine, which you can see in the animation below.