Problem with multipage .stk tiff file

[neo_philiac]

Hi folks:

Has anyone ever tried to dissect a special type of multipage tiff file called .stk or metamorph tiff stack. I have tried libtiff to read it but cant read past the first slice. Of course I am trying to do this in c. There is tiffread.m Matlab file that I am trying to rip thru to get it to work in c but so far failed. Please let me know if anyone has done this before or have any clue :)

Here are a few example of stk files if anyone is interested in giving this a shot.

Below are links to the sample files:
ftp://ftp.meta.moleculardevices.com/support/stack/10xcalib.stk
ftp://ftp.meta.moleculardevices.com/support/stack/bigstk.zip
ftp://ftp.meta.moleculardevices.com/support/stack/calstk.zip
ftp://ftp.meta.moleculardevices.com/support/stack/smstk.zip

Thanks

[BLiZZaRD]

STK Extractor NoLabel (http://cleterrier.net/Macros/STK_Extractor_NoLabel.txt) : this macro allows to batch convert multichannel .stk file made by the "Acquire Multiple Wavelength" mode in Metamorph. It will just convert them to a series of single tif images with a number appended for each channel.



The ImageJ macro language is well suited to automate repetitive tasks and processing workflows. To use one of these macro, just save it as text files from your browser, drop it in your ImageJ plugin folder, and they will appear along your other plugins in the Plugins menu after ImageJ restart.


imageJ Download (http://rsbweb.nih.gov/ij/download.html)

Sounds promising. Never used any of it before, so I can't verify. But it's a start :)

[neo_philiac]

Thank you very much for your response. I am actually currently viewing the images with ImageJ. But the problem is I want to do this all in C since I need to process each slice and then put them back together and speed is an issue for me. Please let me know if there are any other sources in C and by the mean time I will go thru the macro.

[BLiZZaRD]

Sorry, the only thing I know about C is that it comes after B and before D in the English alphabet. :)

[Dino77]

I temporarily worked arround this issue by using the USER0-15
encapsulations, these are handled by the DLT_USER00-15 "dissectors" I
checked in yesterday, in whose preferences one can set which
protocol(s) is(are) carried by each encapsulation. By now each .stk file used by the file is mapped to an USER encap starting from USER0 in the order they appear in the file.