[Insight-users] 16-Bit TIFF and then some

[Greg Soltis]

Greetings,

I work at a mass spectroscopy lab and am interested in:
- First, reading in and stacking hundreds of images in 16-bit TIFF files
- Second, creating a 3D structure/volume from these images, and
- Third, being able to take cross-sections or 3-dimensional sections 
(chunks) out of this volume to analyze the conditions at various regions of 
interest

Since we rely on the quantitative data provided by these images, we cannot 
lose the information originally contained in the data when converting to a 
different file format or in the process of assembling or later dissecting 
this volume.

We are interested in utilizing 16-bit TIFF files that inherently possess 
this quantitative data with a program called 3D Slicer (or if you know of 
another one, we are all ears).

While we have discovered other imaging options/programs and file formats, 
they cannot represent the quantitative information we seek.

I have checked out the past two years worth of archived dialogue on the itk 
users list for what seemed to be pertinent material and have looked through 
the tutorial (The one I find is dated 2005; is there not a newer one?).

But any future effort is moot if we are not able to work with 16-bit TIFF 
files in itk (or vtk). So for starters:

1) Is ITK (and/or VTK) conducive to 16-bit TIFF files?
	I have found options such as vtkTIFFReader, itk::TIFFImageIO, and 
itk::TIFFImageIOFactory. But do they read/accommodate 16-bit files as well 
as 8-bit? (I realize this is an itk list but, if you could enlighten me 
regarding the vtk classes/modules, I would appreciate it; likewise for 
question #2....)


If the answer to #1 is in the affirmative (that 16-bit TIFF files are 
conducive), then the following issues arise:

2) To assemble these hundreds of images, what are the pros/cons of using the 
following? How would the end product be different? Are any of these NOT able 
to use 16-bit TIFF files?
- vtkImageAppend
- vtkVolume16Reader (This one seems ideal.)
- itkImageSeriesReader


3) Does this process involve implementing a few steps (i.e., one to read in 
the tiff files and one to generate a volume from them) or is it much more 
complicated? As I have been learning more and more about the processes and 
programs available, this process is only becoming more complicated.


4) While I have programming experience, it is in Fortran and thus nothing 
comparable to the language used here – as I am sure you can tell by now. 
If this discussion can ultimately determine which classes/modules are 
necessary to provide the desired function stipulated at the onset of this 
message, is there a standard code for each class/module that I can enter 
into the system here at the lab? The time necessary for me to learn the 
code, write it, and implement it would take too long; I have to go back to 
school in a few months :) Can I presume that you have access to such a code 
for reference purposes that serves as a tool when addressing the various 
concerns that come your way? With enough research and dialogue, I can get a 
feel for what needs to be done, but actually doing it is a whole other 
ballgame for which I am not personally qualified.

Thank you very much for your time and advice.

Peace,

Greg

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