[vtkusers] 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.

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

1) Is VTK (and/or ITK) 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 a vtk list but, if you could enlighten me 
regarding the itk 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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