Image conversion

[yuan chen]

Dear All Friend

I am trying to convert voxels of images from microCT images into 8 node finite elements. The requirements is to have the image formats of 16 bits rather than 8bits, so I don't lose information about grayscale.


The sad truth is the reconstruction software can only cope with 16 bit ( original plain photographs) and convert them to 8 bits. Does anyone know that if there is any software ( whether open source or commercial ) which would allow me to make image reconstruction from 16 bit plain tiff photo to 16 bit reconstructed images?

Best wishes

Yuan Chen

University of Sheffield

ychen48@shef.ac.uk

[Dave Gutekunst]

Re: Image conversion

Hi Yuan,

I think that the open-source ImageJ may work for you. It can be downloaded at http://rsb.info.nih.gov/ij/, and there is a very large, responsive user community that has put together large tutorial manuals and is continually adding to the tool's capabilities.

In ImageJ, it is no problem to open TIFF image stacks (File -> Import -> Image Sequence) and to maintain full 16-bit grayscale data, but based on your description, I'm a bit unsure what your desired file output is. Can you provide more detail about what is needed as input for the finite element software?

Good luck!

Dave

[yuan chen]

Re: Image conversion

Dear Dave

Thanks very much for you information.

Sorry I didn't explain myself very well. Basically, My job is to convert the 3D reconstruction images from the CT scan to 8-nodes finite elements with the help of Matlab and ANSYS. Cause I don't want lose too much information about the grayscale, the reconstruction images are better of the format of 16 bits tiff, 16 bit raw or
dicom.

Unfortunately, the reconstruction software in our CT could only cope with the 16 bits plain radiographs and convert it into 8 bits reconstruction dataset, which of course would be useless in my case. So I am wondering if there is some software that could help do the reconstruction the 16 bit plain images and output it as 16 bits tiff images.

Cheers

Yuan

[Seth Gilchrist]

Re: Image conversion

Hi Yuan,
I'm still a bit unclear if the software you are looking for needs to actually *DO* the reconstruction and output 16bit tiffs, or if you have 2D images that were output by a reconstruction algorithm and want to convert them to 16bit tiff. Maybe detailing what a "plain image" is would help. A solution that might work for you (depending on your C++ knowledge) is the Insight Toolkit (itk.org). ITK contains all of the software you need to do reconstructions and convert between image types. There are also Python wrappers for ITK.

It is fairly simple to convert from from one 2D image type to another, and is covered in Chapter 7.5 of their software guide (http://www.itk.org/ITK/help/documentation.html). All you need to do is cast the input image to whatever you want for the output image. There is a well annotated code example on their github site (https://github.com/Kitware/ITK/blob/...dCastWrite.cxx).

If you have Hough space images and want to reconstruct the planar images, I see that Kitware has released the Reconstruction Toolkit (http://www.openrtk.org/) which might help you. I have never used this software.

HTH,
Seth

[yuan chen]

Re: Image conversion

Dear Seth

Thanks very much for your information.

Sorry about the misleading. It is the 2D images that were reconstructed I have got ( 8 bits tiff) , but what I want is the 16 bit tiff images. I don't think it is ok to convert the 8 bit tiff to 16 bits ? ( the gray scale captured from 8 bits tiff has already been lost) . But our scanner technician told me that the only 16 bits images are the plain radiographs before reconstruction, so I will need a software to do the reconstruction and output them as 16 bits tiff myself.

Best

Yuan Chen

[Seth Gilchrist]

Re: Image conversion

Hi Yuan,
Depending on what you are doing with the images, casting them from 8 to 16 bit might work. I would certainly try that - even if it's just to verify the rest of the analysis pipeline - before going through the hassle of getting your own reconstruction working. Unfortunately I don't have any experience with reconstructing CT images, but I'm sure there are places online where you can find assistance with that. In addition to the Kitware link, a quick google turned up three more open source projects:

http://web.eecs.umich.edu/~fessler/code/

http://www.cs.toronto.edu/~nrezvani/OSCaR.html

http://sourceforge.net/projects/openrecon/

Best of luck.
Seth

[yuan chen]

Re: Image conversion

Dear Seth

You right, I will give it a go anyway. The sky scan built-in reconstruction software NRcon might do.

Best

Yuan

[DeQuincey HENSON]

Re: Image conversion

im not sure which image format you wanna convert, anyhow see this image converting program to have a try.