[Insight-users] Re: Images Posted

[Luis Ibanez]

Hi Jessica,

ITK was missing a filter for resampling RGB images,
which is one of the steps required for your program.

We just added a new filter:

         itkVectorResampleImageFilter

Please update your CVS checkout in order to get this
filter. You will find and example on how to use this
filter in the file:


   Insight/Examples/Filtering/ResampleImageFilter6.cxx


Please use this filter intead of the plain itkResampleImageFilter
in order to resample your RGB images.

Note that you don't need 3 dimensions. In ITK the notion
of color channels is represented using the RGBPixel class.
You simply need a 2D image of RGBpixels, like:


    typedef    itk::RGBPixel< unsigned char >   PixelType;
    typedef    itk::Image< PixelType, 2 >       ImageType;


Please let us know if you find any problems,


Thanks


   Luis


------------------------------------
jessica-deryk at uiowa . edu wrote:

> I am composing a mosaic of many small 2D RGB image tiles to make a single 
> image of a complete slice of lung. The images are stereomicroscopic not 
> confocal (but one day the system will hopefully use confocal). A 3D 
> reconstruction of the tissue will be generated from the many 2D slices and the 
> resulting pathology dataset registered with corrosponding CT images.
> 
> I do just need to resample the RGB image. I thought I might have needed three 
> dimensions (for the three channels) I guess i never tried resampling the RGB 
> images with the 2D resample. 
> 
> If i use the ImageReadWrite example, is there a way inwhich I can specify my 
> pixel spacing or should I modify the text file once it is generated?
> 
> Thanks again
> Jessica 
> 
> Quoting Luis Ibanez <luis . ibanez at kitware . com>:
> 
> 
>>Hi Jessica,
>>
>>Thanks for posting your images in MyPACS.
>>It was pretty easy to look at them.
>>
>>I'm confused now if you are using 3D images
>>like in confocal microscopy or you are just
>>composing the mosaic of a large image by
>>stitching the tiles in rows and columns
>>in a 2D grid. Could you please clarify this ?
>>
>> From your last email it looks like you just
>>need to resample the RGB 2D image...
>>is that right ?
>>
>>----
>>
>>If you want to convert the images from one format
>>to another you can simply use the ITK example
>>
>>    Insight/Examples/IO/ImageReadWrite.cxx
>>
>>you can for example read a PNG image and write it
>>as Analyze or MetaImage format.
>>
>>I would suggest you to use MetaImage since the
>>header is in ascii text and it is easy to read.
>>
>>Simply execute the program as:
>>
>>    ImageReadWrite  input.png   output.mhd
>>
>>That will convert your input PNG image into
>>a MetaImage format. You can also read JPEG
>>and TIFF images (if you are using the CVS
>>version of ITK).
>>
>>---
>>
>>Regards,
>>
>>
>>   Luis
>>
>>
>>----------------------
>>Jessica de Ryk wrote:
>>
>>
>>>I have built the adjusted code but am having run time problems when I 
>>>input my images. I get an abnormal program termination (exception 
>>>breakpoint) I have posted an example of two images on the MyPACS.net 
>>>(the case number is 253148)
>>>Maybe I am aproaching final output of producing the cropped tile 
>>>in wrong way? I have many images to tile together to construct a single 
>>>color slice (the 3D was for the color as opposed to grayscale) of lung 
>>>pathology. The overlap is 20% of the image FOV + /-some error caused by 
>>>inaccuracy in the aquisition system. I want to register two images and 
>>>then join them to produce one aligned image. Then register the aligned 
>>>image with the next tile, etc first building up image rows then 
>>>registering the individual rows. I thought this would be very straight 
>>>forward to accomplish. As I am much more familiar with C, I thought I 
>>>could program the organization of the images with respect to eachother, 
>>>and the overall tiling of the images and call my itk based registration 
>>>program to produced the correctly cropped image tiles.
>>>What program would you recomend to convert my images?? Which format is 
>>>better, Analyze or MetaImage
>>>Thanks for your ongoing advice
>>>Jessica
>>> 
>>> 
>>> 
>>>
>>
>>
>>
> 
> 
> 
> 
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