[Insight-users] Re: Images Posted

[jessica-deryk@uiowa.edu]

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
> >  
> >  
> >  
> > 
> 
> 
>