IT-LIST Digest 25Topics covered in this issue include:  1) Re: Axon Imaging Workbench	by "S. Brent Dove"   2) Re: Image Tool source code for Borland C++5.0	by "S. Brent Dove"   3) match up spots in two images	by Greg Blair   4) Re: Counting black and white pixels	by "Emily B. Kim"   5) Re: Counting black and white pixels	by Robert Smith   6) Re: Image Tool source code for Borland C++5.0	by MR SSE KOH   7) Re: Come on, baby, fix your source	by "S. Brent Dove"   8) Re: Gel Analysis	by "S. Brent Dove"   9) Re: Gel Analysis	by "BRADLEY MR GRAEME - EXP. BIOLOGY"  10) Win95 compatibility for DT3155	by Robert O Gappinger  11) WinVFG Driver Standard	by Robert Smith ----------------------------------------------------------------------Date: Fri, 21 Jun 1996 13:01:25 -0500 (CDT)From: "S. Brent Dove" To: IT List Subject: Re: Axon Imaging WorkbenchMessage-ID: <01I666JOO37M006NOA@uthscsa.edu>Recently on ITLIST>Is there a driver for the Digidata2000, that allows aquiring images with IT ?No and none is planed at the present time.  As you can understand we as a development team cannot commit the resources to developing drivers for every image acquistion system that is available. That is why we have developed a simple interface for any manufacturer to create a driver for UTHSCSA ImageTool.  Our source code is freely available and we even provide example code which has been thoroughly tested with the DT3155 from Data Translation plugin.  I can only suggest that UTHSCSA ImageTool users demand that these different acquistion board manufacturer provide the plugin necessary to use ImageTool..  We are ready to work with any company to help them provide this for their customers.S. Brent Dove                            Voice: (210) 567-3333Diagnostic Sciences                      Fax:   (210) 567-3334University of Texas                      Email: dove@uthscsa.eduHealth Science Center                    Web:   ddsdx.uthscsa.eduSan Antonio, TX    USA                   ftp:   maxrad6.uthscsa.edu------------------------------Date: Fri, 21 Jun 1996 13:01:21 -0500 (CDT)From: "S. Brent Dove" To: IT List Subject: Re: Image Tool source code for Borland C++5.0Message-ID: <01I666JLONJU006NOA@uthscsa.edu>Recently on ITLIST>I would like to know if the IT source code is available also for C++ >version 5.0.>>PS: I have problems with downloading ITSDK.ZIP file and I think it has >some errors. Would you please check it for me.First of all we have just concluded the recompilation of UTHSCSA ImageTool using Borlands new C++ 5.0 compiler.  Some new tweaks were necessary and some reorganization of the original code was made.  We will try and have a this alpha version available by June 28th. This will be a true Alpha version and should not be used for research until a more thorough testing can be performed, but it may be useful in starting any development as we will only support this version in the future.As to the second problem, we have had some problems with the zip application corrupting the ITSDK.zip file.  I have since recompressed the file and tested it myself.  As far as I know as of June 1, there should not be a problem.  So long for now.S. Brent Dove                            Voice: (210) 567-3333Diagnostic Sciences                      Fax:   (210) 567-3334University of Texas                      Email: dove@uthscsa.eduHealth Science Center                    Web:   ddsdx.uthscsa.eduSan Antonio, TX    USA                   ftp:   maxrad6.uthscsa.edu------------------------------Date: 	Fri, 21 Jun 1996 12:10:42 -0400From: Greg Blair To: siggraph@dgp.toronto.edu, it-list@sparky.uthscsa.eduCc: sci.image.processing@dgp.toronto.eduSubject: match up spots in two imagesMessage-ID: <31CAC982.57CF@dgp.toronto.edu>Anyone have any thought on how to match up or compare small spots on two images?We have two images taken at different times of the same object.The object can change proportions but the orientation essentially stays the same.  The illumination may be different.  The focal length and distance to object remains constant.We must classify them and then match them up, producing a listof (x,y)'s for the spots on each image that match and are different(disappeared from the second image or new to the second image).To classify them we look for small islands and output a list of (x,y)centroids, major and minor axis, area, and topological euler numberto describe any holes inside a spot, or any spots inside a hole, inside a spot.------------------------------Date: Fri, 21 Jun 1996 11:46:49 -0700 (PDT)From: "Emily B. Kim" To: it-list@sparky.uthscsa.eduSubject: Re: Counting black and white pixelsMessage-ID: <199606211846.LAA19126@franc.ucdavis.edu>Pixel counting routines are pretty standard in any Image Processing>package.  If you don't have such, then IT is a good free IP system.  You can>download it from  http:/ddsdx.uthscsa.edu.>Read the instructions; pixel counting is a little complicated but I just did>it and so can you.thanks for your response, robert, but i've already downloaded it andinstalled it.  i tried using it, and it didn't work.  i can't find anyinstructions for black and white pixel counting.  i've searched the on-linehelp in the program, i've searched the web site, and i've even done somesearches on alta vista to try and find other sources.  so far no luck. :(could you please direct me to the instructions that you mention in your letter?>You don't mention what format your images are in.  You may have to convert>them to a format that IT can handle.  Image Alchemy is a good shareware>conversion program which you can download from shareware.com.my pictures are in .tif format.  as far as i can tell from the documentationthat should work.  i've also tried reducing the image to 8 bit ---- even twobit.  but it still only gave me standard deviation and mean.  sigh.  thanks!-emily  ps...i'll check out image alchemy as you suggested.--Emily B. KimPaper TigerPO Box 74205Davis, CA 95617------------------------------Date: Mon, 24 Jun 1996 12:12:22 -0400From: Robert Smith To: it-list@sparky.uthscsa.eduSubject: Re: Counting black and white pixelsMessage-ID: <1.5.4.32.19960624161222.0067389c@curtech.com>At 03:25 PM 6/21/96 +0600, you wrote:>>>thanks for your response, robert, but i've already downloaded it and>installed it.  i tried using it, and it didn't work.  i can't find any>instructions for black and white pixel counting.  i've searched the on-line>help in the program, i've searched the web site, and i've even done some>searches on alta vista to try and find other sources.  so far no luck. :(>could you please direct me to the instructions that you mention in your letter?>>Emily:  In fact, I think the plug-in is 3rd party and undocumented.  The sequenceof operations I used is:        Open image (I used blobs.tif)        Processing|threshold|manual  (set a reasonable threshold and get a1-bit                  image)`       Plug-ins|run|(at this point change dir to \plug-ins, and runbwcount.dll)        un-minimize the Results window and there's the answer!Good luckBob             .  Robert A. Smith, Ph.D.  _____    .    Vision Systems' Analyst |     |<.      Current Technology, Inc. |_____|   .    (603) 868-2270     ^       .  ras@curtech.com    / \   /   \------------------------------Date: Sun, 23 Jun 1996 15:06:50From: MR SSE KOH To: it-list@sparky.uthscsa.eduSubject: Re: Image Tool source code for Borland C++5.0Message-ID: <4E12FE3C48@novell2.bham.ac.uk>Dear manager,        I am interested to obtain the source code for the image tool.I wonder do you have the source in window version 3.1 or 3.11. If yes, could direct me to the location of the source code. Thank you very much in advance.Best regardsKoh******************************************************University of BirminghamSchool of Manufacturing and Mechanical EngineeringEdgbaston, B15 2TT.                               United Kingdom.                                  EMAIL:MME3SSK0@NOVELL2.BHAM.AC.UK******************************************************------------------------------Date: Fri, 21 Jun 1996 16:01:14 -0500 (CDT)From: "S. Brent Dove" To: IT List Subject: Re: Come on, baby, fix your sourceMessage-ID: <01I66CTM4PD8006NOA@uthscsa.edu>Recently on ITLIST>it's a pitty, no, it's a shame, to have such a nice code in such a bad >condition! Please, do something, our >lives depend on it...>We were desperately trying to unzip THE ITSDK.ZIP but there were a heap of >errors and, at the end, probbably >becouse of all those errors, the lack of some essential files.We have over 5,000 user of UTHSCSA ImageTool World Wide and numerous developers working on ImageTool source code.  We have had some problems with corruption during WINZIP compression of these files.  That was over a month ago, we have not had any problems since that time.  I suggest you download the files again or try to find out the problem at your end.  We have downloaded the SDK and thoroughly tested the decompression of the ZIP files with NO ERRORS.S. Brent Dove                            Voice: (210) 567-3333Diagnostic Sciences                      Fax:   (210) 567-3334University of Texas                      Email: dove@uthscsa.eduHealth Science Center                    Web:   ddsdx.uthscsa.eduSan Antonio, TX    USA                   ftp:   maxrad6.uthscsa.edu------------------------------Date: Fri, 21 Jun 1996 16:01:15 -0500 (CDT)From: "S. Brent Dove" To: IT List Subject: Re: Gel AnalysisMessage-ID: <01I66CTNARN4006NOA@uthscsa.edu>Recently on ITLIST>I would like to know how i can use IT if i want to analyse electrophoresis>gels by densitometry.>When i use the Line profil option, the profil of my gel is satured over 255>scale gray how can i do to obtain a sharp profil of my gel ?First, we are presently writing the design specification of a gel analysis plugin that would support 1D & 2D densitometric gel analysis, molecular weight determination by gel electrophoresis.  WE hope to have the plugin ready by the end of the summer.. If anyone has any suggestions on what the plugin should do please let us know suggestion are welcome but we probably cannot do everything that people want.  We want to do the most good for the most people.Second,  if the line profile indicates that you are saturated over 255 you need to adjust you acquistion parameters to decrease these gray level.  I do not know what type of acquisition device you are using ie. framegrabber or scanner.  Both of these type of image acquisition systems should provide for changing the contrast and brightness to provide a good dynamic range of your gel.S. Brent Dove                            Voice: (210) 567-3333Diagnostic Sciences                      Fax:   (210) 567-3334University of Texas                      Email: dove@uthscsa.eduHealth Science Center                    Web:   ddsdx.uthscsa.eduSan Antonio, TX    USA                   ftp:   maxrad6.uthscsa.edu------------------------------Date: Wed, 26 Jun 1996 14:54:52 GMT-0200From: "BRADLEY MR GRAEME - EXP. BIOLOGY" To: it-list@sparky.uthscsa.eduSubject: Re: Gel AnalysisMessage-ID: > Recently on ITLIST> > >I would like to know how i can use IT if i want to analyse electrophoresis> >gels by densitometry.> >When i use the Line profil option, the profil of my gel is satured over 255> >scale gray how can i do to obtain a sharp profil of my gel ?> > > First, we are presently writing the design specification of a gel > analysis plugin that would support 1D & 2D densitometric gel analysis, > molecular weight determination by gel electrophoresis.  WE hope to have > the plugin ready by the end of the summer.. If anyone has any suggestions > on what the plugin should do please let us know suggestion are welcome > but we probably cannot do everything that people want.  We want to do the > most good for the most people.> I am presently evaluating all software available that does this sort of analysis.  The following are suggestions i would think essential for 1D and  2D analysis.1D analysis:  To generate a standard curve of log molecular weight vs Rf (where Rf is the distance your std band has travelled divided by the distance of the dye front) of your standards, from which the molecular weight of your sample can then be calculated from the linear regression data.  I would also like to determine the relative densities of the bands and then have these translated into a concentration based on the relative density of a known standard concentration run together on the gel.What would also be necessary would be the ability to straighten lanes that run skew as well as automatic identification of the lanes and the bands within the lanes (being able to set the density threshold here would also be useful).2D analysis:  These normally involve the seperation of proteins on isoelectric focusing followed by size seperation.  It would therefore be useful not only to have the facility to calculate the relative molecular weight of each spot but also its isoelectric point.  The calculation of relative concentrations of the spots would also be useful.An additional perk would be the ability to compare the patterns or concentrations from different gels with each other, which would involve a standardisation of each gel based on the standard lane thus making the reference point equal for gels run under different conditions.  Another would be to identify the appearance or disappearance of spots on 2D gels.I hope these suggestions would be useful to you in designing a plug-in and look forward to trying out your programmes.Dr Graeme BradleyHead of Reproductive BiologyExperimental Biology ProgrammeP.O. Box 19070Tygerberg7505Tel: +27-21-9380304  Fax: +27-21-9380456 ------------------------------Date: Wed, 26 Jun 1996 09:05:39 -0700 (MST)From: Robert O Gappinger To: it-list@sparky.uthscsa.eduSubject: Win95 compatibility for DT3155Message-ID: I noticed in an earlier message that Data Translation had released their Win95 drivers and you plan to make IT compatible with Win95 and the DT3155 frame grabber.  Do you have an estimated date of availability for this version?Robert GappingerOptical Sciences CenterUniversity of Arizona------------------------------Date: Wed, 26 Jun 1996 14:24:15 -0400From: Robert Smith To: it-list@sparky.uthscsa.eduSubject: WinVFG Driver StandardMessage-ID: <1.5.4.32.19960626182415.00669d04@curtech.com>Hi:  do you people have any plans to interface to the the New Windows VideoFrame Grabber Standard Driver?  It would seem to me to make a lot of sense.  Also I would then devote myefforts toward meeting this standara, instead of writing a plug-in for IT.  The standard is pretty exhaustive, allowing you access to most any IPoperations a board might have, but I should think that -- at least for afirst cut -- a simple snap-n-grab would be quite sufficient.  If you haven't a copy of this, go toFTP://ftp.std.com/associations/winvfg/ and download the Acrobat-format file(I forget it's name).Bob             .  Robert A. Smith, Ph.D.  _____    .    Vision Systems' Analyst |     |<.      Current Technology, Inc. |_____|   .    (603) 868-2270     ^       .  ras@curtech.com    / \   /   \------------------------------End of IT-LIST Digest 25