IT-LIST Digest 41Topics covered in this issue include:  1) Re: object tracking?	by "Don Wilcox"   2) Re: Problem in the centroid calculation	by "Don Wilcox"   3) Re: Morphological operations	by "Don Wilcox"   4) TWAIN Interface for Integrating CCD Camera	by Jeff Stiegman   5) Re: Analysis of PAGE data from IT	by "Peter D. Cherry"   6) Re: Analysis of PAGE data from IT	by "Michael A. Ferenczi"   7) Re: Morphological operations	by "Dr. Bin Yu"   8) Re: Analysis of PAGE data from IT	by Niceto Munoz   9) "Find objects"	by ramesh  10) Re: Problem in the centroid calculation	by hubert@bert.van.forintek.ca----------------------------------------------------------------------Date: Wed, 28 Aug 1996 13:59:36 -0700From: "Don Wilcox" To: Subject: Re: object tracking?Message-ID: <199608282114.OAA14724@dogbert.xroads.com>----------> From: Shaibani, Sanan > To: wilcox@xroads.com> Subject: object tracking?> Date: Monday, August 26, 1996 11:57 PM> > Is it possible to register, and then track the path of multiple objects ina> sequence of gray scale images to determine the distance the objects has> moved through 15 consecutive frames? There is no mechanism for this built-in to ImageTool.  However, it ispossible to write plug-ins that process the object set in successive imagesin a stack, so this could be done as a plug-in.> > I am using IT 1.25 and have yet to determine how use the stack functionto> link information from one frame to the next.There is very little built-in support for this in ImageTool, since thenature of the information needed between frames is so broad andapplication-specific.Don------------------------------Date: Wed, 28 Aug 1996 16:36:59 -0700From: "Don Wilcox" To: Subject: Re: Problem in the centroid calculationMessage-ID: <199608282351.QAA18022@dogbert.xroads.com>> I think there is asmall  bug in the centroid calculation routine.  I > disovered it by finding the centroid of a square having a sharp edge > normal to one of the face of the square as illusatred below:> >                   _________>                  !                 !>                  !                 !>                  !                 !******>                  !________!> I do not understand.  Could you give me more details?  Perhaps you have animage that I could use to check for the bug?Thanks,Don------------------------------Date: Wed, 28 Aug 1996 16:38:23 -0700From: "Don Wilcox" To: Subject: Re: Morphological operationsMessage-ID: <199608282351.QAA18025@dogbert.xroads.com>> I tested on the sample image blobs.tif. Any one of four morphological> operations results in reverse of black pixels around the binary image> boundaries. No any effect to the objects in the image. BTW, the polygon> for AOI in this operation is in white color which is not obvious in a> binary image.I do not understand.  Are you saying that the objects are white and notblack?  If so, then the morph operators will not work correctly.  Otherwise,could you be more specific?Thanks,Don------------------------------Date: Wed, 28 Aug 1996 20:01:19 -0400From: Jeff Stiegman To: IT-LIST Subject: TWAIN Interface for Integrating CCD CameraMessage-ID: <3224DDCF.30F5@mail.msen.com>BioPhotonics offers a CCD camera/framegrabber kit which utilizes a TWAIN source driver for camera exposure control and image capture functions.  We have successfully tested this package with the TWAIN interface provided in ImageTool V1.25.The TWAIN driver was developed specifically for low light applications which require extended exposure durations.  It features automatic or manual exposure selections up to 30 minutes, LUT manipulation for positive/negative view, and an  "over exposure" indicator.  Direct printer support is also provided for the SONY UP-D860 255 grayscale printer.The TWAIN Camera Kit is available with both cooled and non-cooled CCD cameras, ISA or PCI bus, and currently supports 8 bit image capture.  A 10 bit version will be available November 1, 1996.Cat # 5105  TWAIN Non-Cooled Camera Kit for PC 	$3,515includes:  	BP-M1 CCD Integrating Camera	1Mb 8 bit Framegrabber/VGA Graphic Card (ISA Bus)	Cable Kit & TWAIN Driver SoftwareCat # 5110  TWAIN Cooled Camera Kit for PC	$4,015includes:	BP-M1C Peltier Cooled CCD Integrating Camera 	1Mb 8 bit Framegrabber/VGA Graphic Card	Cable Kit & TWAIN Driver SoftwareFor more information e-mail a request to BioPhotonics at [bpc@msen.com].------------------------------Date: Wed, 28 Aug 1996 20:11:51 -0400From: "Peter D. Cherry" To: it-list@sparky.uthscsa.eduSubject: Re: Analysis of PAGE data from ITMessage-ID: <3224E046.481E@scisun.sci.ccny.cuny.edu>Andy Phillips wrote:> > Hi,> > I'm looking for software to help analyze my autorads of Northern blots. I> downloaded ImageTool and found the function for producing a line profile> and for saving the data to file. Now I need a program that can read the> data from the line profiles and integrate the area under each peak, with> the facility to set the background level. Can anyone suggest software to> achieve this?> > Thanks.> > Andy Phillips> >  ------------------------------------------------------------------------>  Email  : andy.phillips@bbsrc.ac.uk  : University of Bristol>  Home   : andy@cycad.demon.co.uk     : IACR Long Ashton Research Station>  Phone  : +44-1275-549257            : Long Ashton>  Fax    : +44-1275-394281            : Bristol, BS18 9AF, UK>  WWW    : http://www.lars.bbsrc.ac.uk/plantsci/molbiol/andy.html>  ------------------------------------------------------------------------There is a commercial program called Unscanit by a company called SilkScientific.  It can read in pcx files and using automatic line followingtechniques, generate ascii tables of the line profile.  These may beimported into any spreadsheet or graphing program.  In addition it has abuilt-in intergrator function allowing area under curve determinations.The program can compensate for non-level baselines and can function inarbitrary or real calibration units. However, it is quite expensive(~$400.00).  If you cannot afford this, it would seem that Image toolcould give you even better quality info on particular gel bands usingobject analysis.  A band detected by thresholding and find objects canbe measure for integrated density.  The total pixel density is a betterestimate, since it does not represent an arbitrarily selected cutthrough the band obtained using line profile.------------------------------Date: Thu, 29 Aug 1996 09:36:05 +0100From: "Michael A. Ferenczi" To: it-list@sparky.uthscsa.eduSubject: Re: Analysis of PAGE data from ITMessage-ID: <1.5.4.32.19960829083605.0068c6cc@nimsb41.nimr.mrc.ac.uk>I recommend Jandel's PeakFit program. Expensive perhaps, but works greatAt 01:22 PM 28-08-96 +0600, you wrote:>Hi,>>I'm looking for software to help analyze my autorads of Northern blots. I >downloaded ImageTool and found the function for producing a line profile >and for saving the data to file. Now I need a program that can read the >data from the line profiles and integrate the area under each peak, with >the facility to set the background level. Can anyone suggest software to >achieve this?>>Thanks.>>Andy Phillips>> ------------------------------------------------------------------------ > Email  : andy.phillips@bbsrc.ac.uk  : University of Bristol> Home   : andy@cycad.demon.co.uk     : IACR Long Ashton Research Station > Phone  : +44-1275-549257            : Long Ashton> Fax    : +44-1275-394281            : Bristol, BS18 9AF, UK> WWW    : http://www.lars.bbsrc.ac.uk/plantsci/molbiol/andy.html> ------------------------------------------------------------------------>>Mike Ferenczihttp://npbsn41.nimr.mrc.ac.uk------------------------------Date: Thu, 29 Aug 1996 09:19:59 -0400From: "Dr. Bin Yu" To: it-list@sparky.uthscsa.eduSubject: Re: Morphological operationsMessage-ID: <322598FF.45AA@cps.msu.edu>Don Wilcox wrote:> > > I tested on the sample image blobs.tif. Any one of four morphological> > operations results in reverse of black pixels around the binary image> > boundaries. No any effect to the objects in the image. BTW, the polygon> > for AOI in this operation is in white color which is not obvious in a> > binary image.> I do not understand.  Are you saying that the objects are white and not> black?  If so, then the morph operators will not work correctly.  Otherwise,> could you be more specific?> > Thanks,> > DonIn my practice, all morph operators don't work. The change we can seeafter applying one of four operators to a binary image once or multipletimes is that the pixels around the image four boundaries become white.Nothing happen to almost whole image.Thanks,Bin------------------------------Date: Thu, 29 Aug 1996 16:18:20 +0100From: Niceto Munoz To: it-list@sparky.uthscsa.eduSubject: Re: Analysis of PAGE data from ITMessage-ID: <199608291518.QAA12253@master.ivia.es>>I'm looking for software to help analyze my autorads of Northern blots. I >downloaded ImageTool and found the function for producing a line profile >and for saving the data to file. Now I need a program that can read the >data from the line profiles and integrate the area under each peak, with >the facility to set the background level. Can anyone suggest software to >achieve this?Hi, AndyI was looking for the same some months ago, on the Net.There are some commercial programs for this purpose, check Jandel www server(http://www.jandel.com) for the "Peakfit" program, It seems very nice. Also,there is a Free program (peaks.exe) initially designed to integrateChromatograms, but I think it will work with your data. You can downloadfrom "ftp://dogwood.botany.uga.edu/pub/Malmberg/Peaks05.intel.zip" Thisprogram only works under W95 or NT, is a text program.I am interested in C code or algorithms to detect peaks in chromatograms orSpectra, if anyone in the list has info, please send to my mail address.I have also writen some "C" functions to acquire data, detect peaks, findmaxima, integrate and output graph to screen, If anybody is interested dontdoubt to mail me.Hope usefull,    NI------------------------------------------------------------------------------Dr. Niceto Munoz               | Voice: +34-6-1391000             o/   >@   Dept. Citricultura IVIA        | Fax:   +34-6-1390240            /O     #   |/Apartado Oficial               | E-MAIL:nmunyoz@master.ivia.es   _|_    (###)46113 Moncada, Valencia, Spain | http://www.ivia.es/~nmunyoz/index.html  / \------------------------------------------------------------------------------------------------------------Date: Thu, 29 Aug 1996 10:08:23 -0700 (PDT)From: ramesh To: it-list@sparky.uthscsa.eduSubject: "Find objects"Message-ID: Hi guyscan somebody help me here ?I am working on mechanical properties of fibre-reinforced composites; and I tried using the "find objects" command on the black & white image (obtained from a color image which has a non-equalized histogram).  Any of the three methods (manual thresholding, automatic or no thresholding) does not seem to work.  A window appears saying that " too many objects.  Change thresholding parameters".   The same thing happens even if I use "smooth a lot" filter.What exactly are thresholding parameters ? And how do I make the ITools find objects before I can start analysis and classification ?ThanksRamesh ------------------------------Date: Thu, 29 Aug 1996 11:40:02 +0000From: hubert@bert.van.forintek.caTo: it-list@sparky.uthscsa.eduSubject: Re: Problem in the centroid calculationMessage-ID: <9608291903.AA17940@sparky.uthscsa.edu>--Message-Boundary-26414Content-type: text/plain; charset=US-ASCIIContent-transfer-encoding: 7BITContent-description: Mail message body> Date:          Wed, 28 Aug 1996 18:45:58 +0600> Reply-to:      it-list@sparky.uthscsa.edu> From:          "Don Wilcox" > To:            hubert@bert.van.forintek.ca> Subject:       Re: Problem in the centroid calculation> > I think there is asmall  bug in the centroid calculation routine.  I > > disovered it by finding the centroid of a square having a sharp edge > > normal to one of the face of the square as illusatred below:> > > >                   _________> >                  !                 !> >                  !                 !> >                  !                 !******> >                  !________!> > > I do not understand.  Could you give me more details?  Perhaps you have an> image that I could use to check for the bug?> > Thanks,> > Don> Don,I send you a image file (centroid.zip) (100x100 pixels)  containing one object :  the centroid of this object is located at (46.38,45.89) whith the origin located at the bottom left corner.  IT found a centroid of (59,52).>From the help of IT, the method to calculate the centroid appears to be OK:x_centroid = sum (x_pixel)/n_pixelsy_centroid = sum (y_pixel)/n_pixelsThe summation includes all pixels of the object.  I suspect you only consider the pixels of the object contour ??Thank you,Pascal --Message-Boundary-26414Content-type: text/plain; charset=US-ASCIIContent-description: Information about this message.This message contains a file prepared for transmission using theMIME BASE64 transfer encoding scheme. If you are using PegasusMail or another MIME-compliant system, you should be able to extractit from within your mailer. If you cannot, please ask your systemadministrator for help.   ---- File information -----------     File:  centroid.zip     Date:  29 Aug 1996, 11:32     Size:  562 bytes.     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