What exactly represents a voxel after loading an image into an array/matrix?

I know a voxel represents a grid in 3d space, but what exactly voxel is when we load an image(s) in matrix? I am not sure but if I load an image in array/matrix foo, then foo(1,1,1) represents a voxel? Is it necessary to load an images(s) in 3d matrix/array?

Will anybody please clear my basic concept by giving a simplest example, I am newbie to matlab and image processing!

Answer 1

[Image Analyst]

A voxel represents some attribute of your sample at a 3-D location. For example, it could be the radiographic density, or the signal from an MRI instrument, or the color of a fluorescent material, or whatever.

[Nitinkumar Ambekar]

I didnt get it sir, do you mean after loading an image into 3d array, each element is a voxel, as I asked in question foo(n,n,n)? In shot, just tell me how to access a voxel?

[Image Analyst]

Yes, that's correct. The voxel value is gotten by specifying the indexes for row, column, and slice, channel, plane or whatever you want to call the third spatial dimension.

voxelValue = array3d(row, column, slice);

A color image is also 3D but since the third dimension represents all the same spatial location, just different spectral values, a color image pixel is not called a voxel. A voxel means that there is a spatial variation along the "z" dimension.

Answer 2

[Guillaume]

It all depends what sort of image you're loading. I'm not familiar with 3d image formats at all but the image formats I'm familiar with (bmp, png, jpeg, etc.) only hold 2D data but may result in a 3d array in matlab because the 3rd dimension is used to store the colour information (rgb triplet).

I suppose with a 3d format, you'd either get a 3d array if the image is greyscale / indexed, or a 4d array if the image is colour.

[Nitinkumar Ambekar]

I am using .dcm images, which is 2d, I loaded it in 3d array, I have to process on each voxel (voxel classification), I am confused here what actually voxel means in this array? Is it single element in array called voxel?

[Guillaume]

If you loaded a single DICOM image and the result is a 3d array, then you have a 2d image with colour information in the third dimension. Therefore there are no voxels, only pixels.

According to dicomread documentation "multiframe images are always 4-D array".

To get voxels, you would have to load several images and concatenate them as a 4d array:

img3d = cat(4, img1, img2, img3, ...);

The voxels would then be img3d(X, Y, :, Z). You could permute the dimensions so that colour is in the 4th dimension rather than the 3rd.

[Nitinkumar Ambekar]

Thanks, that's what I want to know, I have loaded several images into 3d array. But I didn't get one point, why we need 4d to have voxels, why it doesn't happen with 3d?

[Nitinkumar Ambekar]

I request you to add description given in above comment in your answer, so that it'll be helpful for others, I will definitely would like to accept it as answer. Thanks once again.

[Guillaume]

Right, if you have loaded several 2d greyscale images into a 3d array, then yes, each element of the 3d array is a voxel.

You need a 4d array if the images have colour, since you need to store 3 colours per voxel.

[Image Analyst]

Nitinkumar, what are your images from? Four dimensional color images are fairly uncommon. They might arise for example if you were doing color confocal microscopy where you have a full color image at a variety of "z" levels through the depth of your sample. Like Guillaume and I said, a regular color image is 3-D (say 1080 rows by 1920 columns by 3 color channels for HDTV) but the elements are called pixels, not voxels. If you had multiple gray scale images taken at a variety of slice levels, like in a medical CT or MRI image, say 1024 rows by 1024 columns by 512 slices, then that would be a volumetric image and the elements would be called voxels. Exactly what are type of image(s) are you dealing with?

[Nitinkumar Ambekar]

Thank you so much, both of you. Now I got it. I am working on a project in which I have to classify voxels in .dcm DICOM images, I have loaded these images in 3d array.

[Walter Roberson]

dicom arrays are usually 2D arrays of data, and the data is often not in the range expected for pixels. You usually have to recenter and scale if you want pixel values. You might choose to impart false colors according to the data, but the data in dicom data is seldom inherently representing color.