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

[Ruben Schilling]

Sorry for the typo:

ITK does provide the possibility to write TIFFs in 8bit and  
--------------------> 16bit <---------------------------------- (as  
far as you ar [......]


Am 19.06.2007 um 21:34 schrieb Ruben Schilling:

> Hi Greg,
>
> I can tell you from a little bit from my experience about your TIFF  
> plans:
>
> ITK does provide the possibility to write TIFFs in 8bit and 32bit  
> (as far as you are concerned with grayvalue images, I don't know  
> anything about color TIFF's in ITK). There is one strange thing  
> though: I had an issue reading 16 bit images written by ITK with  
> ImageJ. I found, that when I read 16bit images I had to move thru  
> an arbitraey slice (though not the very first one) and reset the  
> threshold value to get the correct picture. I don't know what is  
> wrong with it, either the problem is within ImageJ or ITK, though  
> since ImageJ didn't seem to have similar problems with any other  
> images I would be slightly tempted to blame it on ITK. Though I  
> know, that you will have trouble finding a single application that  
> does really implement the Adobe TIFF 6.0 specification straight by  
> the book or even close to complete.
>
> Certainly many people would advise you to switch to a format like  
> the meta image format or DICOM to save annotation information along  
> with you image and support high bit numbers. Those formats are not  
> supported by as many image readers/viewers though and I found the  
> meta image format to be slower. I guess for archiving images you  
> could just as well use a database to store the annotation and just  
> use a convenient file format as TIFF.
>
> Regarding your question about saving images: That is very easy with  
> ITK. Just look at the sofware guide (pdf online) how the do it,  
> there is a factory class for writing (and reading) images, that  
> determines the image format by the file extension (.tif). Reading  
> and writing images with ITK requires only very few lines of code.
>
> Best regards
> Ruben
>
> Am 19.06.2007 um 21:02 schrieb 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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