http://imagej.273.s1.nabble.com/what-s-the-best-way-to-process-3D-image-data-in-ImageJ-tp5013349p5013374.html
I'll check it out.
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> On 1 Jul 2015, at 04:17, Thomas Boudier <
[hidden email]> wrote:
>
> Dear Shameem,
>
> In my plugin ellipsoid fitting there is angles calculation, I did not test it much but should work.
>
>
http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:3d_analysis:start>
> Best
>
> Thomas
>
>> On 30/06/15 19:53, Shameem Sampath wrote:
>> Hi List,
>> Coincidentally, I have a related query regarding analysing CAT scan Dicom images of knees in ImageJ.
>> Is there a way to measure trabecular orientation in the xyz planes?
>> Regards,
>> Shameem Sampath
>> The Bluespot Knee Clinic
>>
>>
>>> On 30 Jun 2015, at 04:52, Thomas Boudier <
[hidden email]> wrote:
>>>
>>> Dear Zhou Xin,
>>>
>>> Yes ImageJ is not very developer-friendly for 3D processing. I released a basic tutorial for 3D in ImageJ years ago, it may be a bit outdated but give basic notions :
>>>
>>>
http://imagejdocu.tudor.lu/doku.php?id=tutorial:working:3d_image_processing_and_analysis_with_imagej>>>
>>> The guys from ImageJ2 did a great job in redesigning image format for multidimensional images, in the imglib2 library :
>>>
>>>
http://fiji.sc/ImgLib2>>>
>>> I did not have the time to dig into this library, because I use my own library ;)
>>>
>>>
http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start>>>
>>> In ImageJ there is the function getVoxels from ImageStack, it is noted "experimental" but works well I think.
>>>
>>> Here some information, hope this helps.
>>>
>>> Best
>>>
>>> Thomas
>>>
>>>
>>>> On 29/06/15 22:41, 周鑫 wrote:
>>>> 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
>>>>
>>>>
>>>>
>>>> --
>>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>>
>>>> --
>>>> /***************************************************************/
>>>> Thomas Boudier, Associate Professor, UPMC,
>>>> Université Pierre et Marie Curie, Paris, France.
>>>> BioInformatics Institute (BII)/IPAL, Singapore.
>>>> /**************************************************************/
>>> --
>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
> --
> /***************************************************************/
> Thomas Boudier, Associate Professor, UPMC,
> Université Pierre et Marie Curie, Paris, France.
> BioInformatics Institute (BII)/IPAL, Singapore.
> /**************************************************************/
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html