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2010.03.08 16:34 "Re: Problem with multipage .stk tiff file", by Shafiq Abedin
Hi folks, 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 On Mar 8, 2010, at 10:24 AM, Shafiq Abedin wrote: > Hi, > > Since no one has responded with as explanation regarding reading a .stk > file with libtiff, I am assuming you cant. I am looking into the matlab > tiffread2.m file and trying to figure out how to do it without libtiff. If > anyone has any suggestion, please let me know. It will be very helpful to > me if you do :) > > Thnaks > > -- > Shafiq Abedin > > University Of Pittsburgh > McGowan Institute for Regenerative Medicine > > > On Mar 5, 2010, at 8:57 AM, Shafiq Abedin wrote: > >> Great source! I apologize if I sound arrogant but I am trying to >> accomplish this with libtiff and c. We already process our data with >> Matlab. Thank you though :) >> >> >> Shafiq Abedin >> sha33@pitt.edu >> >> >> >> >> On Mar 5, 2010, at 7:46 AM, Ashish Uthama wrote: >> >>> Information in this thread might be useful: >>> http://www.mathworks.com/matlabcentral/newsreader/view_thread/265330 >>> >>> points to: http://support.meta.moleculardevices.com/docs/t10243.pdf and >>> ftp://ftp.meta.moleculardevices.com/support/stack/STK.doc >>> >>> >>> >>> From: tiff-bounces@lists.maptools.org >>> [mailto:tiff-bounces@lists.maptools.org] On Behalf Of Shafiq Abedin >>> Sent: Thursday, March 04, 2010 10:37 PM >>> To: tiff@lists.maptools.org >>> Subject: [Tiff] Problem with multipage .stk tiff file >>> >>> Hello All: >>> >>> I am writing this post after pulling my hair multiple times (I am bald >>> now!) and doing many many google searches (all the webpages related to >>> libtiff is now imprinted in my brain). I have failed to find a post on >>> this mailing list that solves the problem or anywhere for that matter. I >>> hate to be repetitive but I have the same problem described in this post >>> (http://www.asmail.be/msg0054982856.html). Solution given here is too >>> vague for me to pick up on (is it really like a linked list?). I didn't >>> find any post related to reading the .stk file (I wish I could give you >>> a sample right now but they are extremely big - 2gb ). I can read the >>> first in the stack but cant go beyond that. This particular image has >>> 7400 slices but whenever i do a tiffdump, this is what I get: >>> >>> test.stk: >>> Magic: 0x4949 <little-endian> Version: 0x2a >>> Directory 0: offset 1342567917 (0x5005f5ed) next 0 (0) >>> SubFileType (254) LONG (4) 1<0> >>> ImageWidth (256) LONG (4) 1<348> >>> ImageLength (257) LONG (4) 1<260> >>> BitsPerSample (258) SHORT (3) 1<16> >>> Compression (259) SHORT (3) 1<1> >>> Photometric (262) SHORT (3) 1<1> >>> ImageDescription (270) ASCII (2) 2545600<Acquired from Photometri ...> >>> StripOffsets (273) LONG (4) 24<8 7664 15320 22976 30632 38288 45944 >>> 53600 61256 68912 76568 84224 91880 99536 107192 114848 122504 130160 >>> 137816 145472 153128 160784 168440 176096> >>> SamplesPerPixel (277) SHORT (3) 1<1> >>> RowsPerStrip (278) LONG (4) 1<11> >>> StripByteCounts (279) LONG (4) 24<7656 7656 7656 7656 7656 7656 7656 >>> 7656 7656 7656 7656 7656 7656 7656 7656 7656 7656 7656 7656 7656 7656 >>> 7656 7656 4872> >>> XResolution (282) RATIONAL (5) 1<72> >>> YResolution (283) RATIONAL (5) 1<72> >>> PlanarConfig (284) SHORT (3) 1<1> >>> ResolutionUnit (296) SHORT (3) 1<2> >>> Software (305) ASCII (2) 18<MetaMorph 7.1.7.0\0> >>> DateTime (306) ASCII (2) 21<2009:09:08 17:54:57\0\0> >>> Predictor (317) SHORT (3) 1<1> >>> 33628 (0x835c) LONG (4) 7435<0 0 1 0 2 4095 3 0 4 1341649855 5 >>> 1341649863 6 1341649871 7 1341649880 8 0 9 255 11 128 12 64 ...> >>> 33629 (0x835d) RATIONAL (5) 7400<0 0.0383822 0.0380645 0 0.0383822 >>> 0.0380645 0 0.0383821 0.0380645 0 0.0383821 0.0380645 0 0.038382 >>> 0.0380645 0 0.038382 0.0380645 0 0.038382 0.0380645 0 0.0383819 >>> 0.0380645 ...> >>> 33630 (0x835e) RATIONAL (5) 7400<0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 >>> 0 0 0 0 ...> >>> 33631 (0x835f) LONG (4) 7400<28 65536 0 65536 0 65536 0 65536 0 65536 0 >>> 65536 0 65536 0 65536 0 65536 0 65536 0 65536 0 65536 ...> >>> >>> My attempt to get the the read Strip or Tile have failed because the >>> libtiff TIFFTAG_TILEBYTECOUNTS and TIFFTAG_STRIPBYTECOUNTS returns >>> only 24. Although I can see the offset info in the dump, I dont know >>> actually how to get to the next image and read (using TIFFReadScanline) >>> it so that I can manipulate it. I should also mention that the directory >>> count is useless here because it returns 1 . This problem might be too >>> trivial for you but I need help finding a way to read these images. If >>> you please provide examples, it would be most helpful. Thanks in >>> advance. >>> >>> -- >>> Shafiq >>> >>> University Of Pittsburgh >>> McGowan Institute for Regenerative Medicine >>> _______________________________________________ >>> Tiff mailing list: Tiff@lists.maptools.org >>> http://lists.maptools.org/mailman/listinfo/tiff >>> http://www.remotesensing.org/libtiff/ >> >> _______________________________________________ >> Tiff mailing list: Tiff@lists.maptools.org >> http://lists.maptools.org/mailman/listinfo/tiff >> http://www.remotesensing.org/libtiff/ > > _______________________________________________ > Tiff mailing list: Tiff@lists.maptools.org > http://lists.maptools.org/mailman/listinfo/tiff > http://www.remotesensing.org/libtiff/