http://imagej.273.s1.nabble.com/what-s-the-best-way-to-process-3D-image-data-in-ImageJ-tp5013349p5013350.html
Yes ImageJ is not very developer-friendly for 3D processing. I released
> Hi all,
>
>
> I wonder what is the best way to process 3D image data in ImageJ.
> More and more medical images are produced in 3D, such as CT, MRI series....
> In imageJ, the commonly used way is ImageStack (I guess).
> But after reading the StackProcessor and StackConverter, I have some questions:
>
>
> 1: it is important to switch the data between sagittal plane, coronal plane and transverse plane.
> I know that "stacks -> orthogonal views" can show three views at the same time.
> But from data processing point of view, sometimes we need to switch the whole stack from transverse view to sagittal views.
> I means, in matlab, we can use "permute" or "shiftdim" to just change the order of dimensions.
> In stackProcessor or stackConverter, I didn't find similar functions.
>
>
> 2: it is also important to do normalization of resolution.
> For example, a commonly used function is to normalize the stack to be 1x1x1mm voxel.
> In stackProcessor, there are "scale" and "resize", but non of them do z-axis interpolation. (They are just a loop of 2D resize)
> So my question is: what's the difference between "scale" and "resize" ?
> and what's the best way of doing normalization of resolution?
>
>
> 3: in 2D processing，we can use getFloatArray() to get the image in form of float[][]
> in 3D prcessing, can we use getVoxels to get the image in form of float[][][] ?
>
>
> Sorry if these questions are too basic.
>
>
> Best regards, Zhou Xin
>
>
>
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> --
> /***************************************************************/
> Thomas Boudier, Associate Professor, UPMC,
> Université Pierre et Marie Curie, Paris, France.
> BioInformatics Institute (BII)/IPAL, Singapore.
> /**************************************************************/