IT-LIST Digest 20Topics covered in this issue include:  1) trace measure	by James Zheng   2) Pointers to Image Information	by Pablo deTorres   3) Re: Zip-Files	by "Heberto Ghezzo"   4) Re: Zip-Files	by Christopher Hyatt   5) RE: Plugin Development	by J.Glenn@ee.qub.ac.uk  6) UTHSCSA ImageTool Mirror Sites	by "S. Brent Dove"   7) RE: density measurements and immage  reversal	by Don Wilcox   8) measuring lesion area on leaves	by Gregory Forbes   9) NT/ImageTool running slowly	by dcm@image.bio.bnl.gov (Denise Monteleone) 10) problem to capture image	by Gilles Leduc  11) Re: IT 1.23	by Jeff Eriksen  12) Separation of objects	by "S. Brent Dove" ----------------------------------------------------------------------Date: Mon, 29 Apr 1996 14:27:16 -0400From: James Zheng To: "'it-list@sparky.uthscsa.edu'" Subject: trace measureMessage-ID: <01BB35D8.23E77500@rwj-cs-slip06.UMDNJ.EDU>Hello,I am trying to use IT to do some quantitative measurements of nerve =cells in microscopic images.  One thing is to measure the trajectory of =a nerve process.  I found out that IT can not do a trace measure, in =which case you click and hold down left mouse button to trace the =trajectory.  The "distance" function certainly can do it but is very =inconvenient.  Is IT going to add this feature or Is there a plug-in for =this?  It should be also nice if one can trace-measure an area.  It =would be better if one can set the interval between pixels during =trace-measure. =20James ZhengUMDNJ-RWJMSDept. of Neurosci. and Cell Biol. =20------------------------------Date: Mon, 29 Apr 1996 16:48:07 -0400From: Pablo deTorres To: IT-LIST@sparky.uthscsa.eduSubject: Pointers to Image InformationMessage-ID: <2.2.32.19960429204807.0068f014@ix.netcom.com>I am just getting started in image analysis and would appreciate peoplepointing me in the right direction for help, tools, usenet groups and otherresources.Our project involves determining the two dimensional deformation across thesurface of a planar specimen and then calculating strain. We use specklemethods to detect and measure movements to 1/20th of a pixel. We are lookingat objects ranging from micro chips to bones to car doors. I am looking forhelp with:1. Displaying (on the screen) the banded contours or iso lines in atransparent manner as an overlay on the original image.2. Calibration methods to convert pixels to engineering units (inches, mm)across the field of view, To compensate for magnification, distortion  andangularity. We are currently exploring analysis of standard targets(patterns, grids,...)We use the DT3155 board3. Anybody familiar with the MRT professional video PCMCIA frame grabber?Thank you very much!Pablo D. deTorres------------------------------Date:          Tue, 30 Apr 1996 08:43:37 EST5EDTFrom: "Heberto Ghezzo" To: it-list@sparky.uthscsa.eduSubject: Re: Zip-FilesMessage-ID: <199604301248.IAA21326@sirocco.CC.McGill.CA>The  ITSDK.ZIP file has problems!!!I tried to unzip it with the latest pkunzip 32 program and it complains of corrupt CRC in p1prop~1.h it is 000000 should be 195fabc6or something like that.Then I opened the zip file with a 3 years old XTreeGold and I was able to unzip files by subdirectories. In the DLLs/Inc there are 2 files, the p1prop~1 and another one with length of ZERO, these are the files that can not be unzipped.Winzip 6.0 unfortunately can not unzip any file after these files in the listing..R. Heberto Ghezzo  Ph.D.Meakins-Christie LabsMcGill UniversityMontreal - Canadaheberto@meakins.lan.mcgill.ca------------------------------Date: Wed, 1 May 1996 01:12:52 -0400 (EDT)From: Christopher Hyatt To: it-list@sparky.uthscsa.eduSubject: Re: Zip-FilesMessage-ID: I was able to unzip the files in ITSDK.ZIP okay (using XTreeGold 4.0), but I found the same problem with a couple of the files. The names are actually piprop~1.h and piutil~1.h and both are of length zero as stored in the zip file. All other files unzipped okay as far as I can tell.I suspect that since those two files have long filenames (per Windows 95) then whatever ZIP program was used didn't compress them correctly .... however, there are some bitmap files (*.BMP) that appear to have long filenames and they are not of length zero and are intact and can be read by graphics software just fine. Maybe someone with intact versions of piprop~1.h and piutil~1.h can rezip them. I would think PKzip should still be able to store them, but it won't be able to translate the long filenames. An idea is to rename those small number of files with long filenames so they are the eight-dot-three scheme and we all can use a non bugfilled PKZip 2.04g to unzip them. Hope this helps.Christopher HyattUNC-Chapel HillDept. of Medicine/CardiologyOn Tue, 30 Apr 1996, Heberto Ghezzo wrote:> The  ITSDK.ZIP file has problems!!!> I tried to unzip it with the latest pkunzip 32 program and it > complains of corrupt CRC in p1prop~1.h it is 000000 should be 195fabc6> or something like that.> Then I opened the zip file with a 3 years old XTreeGold and I was able > to unzip files by subdirectories. In the DLLs/Inc there are 2 files, > the p1prop~1 and another one with length of ZERO, these are the files > that can not be unzipped.> Winzip 6.0 unfortunately can not unzip any file after these files in > the listing.> .> R. Heberto Ghezzo  Ph.D.> Meakins-Christie Labs> McGill University> Montreal - Canada> heberto@meakins.lan.mcgill.ca> ------------------------------Date: Wed, 1 May 96 10:48:47 BSTFrom: J.Glenn@ee.qub.ac.ukTo: it-list@sparky.uthscsa.eduSubject: RE: Plugin DevelopmentMessage-ID: <9605010948.AA21646@tesla>DonCreating the import library from UTILib32.dll worked. The only thing is the dllI created was a lot larger in size than the one supplied with ImageTool. Evenso it worked! Thanks againJohnny Glenn------------------------------Date: Wed, 01 May 1996 08:01:35 -0600 (CST)From: "S. Brent Dove" To: IT Announce ,Subject: UTHSCSA ImageTool Mirror SitesMessage-ID: <01I46N7C3VJG005MIF@uthscsa.edu>Hello IT Users,Since the introduction of UTHSCSA ImageTool, we have been overwhelmed with the response.  To date we have distributed over 4,000 copies world wide.  We have delivered an update approximately every three months.  We hope to continue to add new features and correct any bugs as soon as possible.  A common problem has been with our server and access to the ftp site.  We have just upgraded our server to a Pentium based Windows NT Server (3.51) and the new Microsoft Internet Information Server (IIS).  We hope that this will improve access and speed significantly.  We have also been able to establish two excellent mirror sites.Thanks to Dave Ingles at HENSA and James McCudden at the Washington University Archive we now have a mirror site in the UK and the USA.  I hope that this will help ImageTool users in the Workld Wide.  Please let me know how this works out.  You can access the HENSA mirror site for UTHSCSA ImageTool at WWW :    gopher://micros.hensa.ac.uk:70/11/mirrors/other/uthscsa/FTP :    ftp://micros.hensa.ac.uk/mirrors/other/uthscsa/Gopher : gopher://micros.hensa.ac.uk:70/11/mirrors/other/uthscsa/Modem :  UK (01524) 843878, cd mirrors/other/uthscsa/ Access via www, ftp, and gopher is restricted to .ac.uk sites during 0800 hours - 2000 hours GMT.>From 2000 hours - 0800 hours GMT, any internet site can access this service.You can access the Washinton University Archivehttp://wuarchive.wustl.edu/packages/graphics/image-tool/ Try our site again or either of these two archives. I hope that UTHSCSA ImageTool will help your research efforts.  Please continue to send in your suggestions for new features and your applications this is the best way to help us develop what you need. So long for now and thank you for your support.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, 1 May 1996 17:12:24 -0700From: Don Wilcox To: 'ImageTool List Server' Subject: RE: density measurements and immage  reversalMessage-ID: <01BB3781.7C6ABF20@ppp.xroads.com>----------From:  NEAL MUSTO[SMTP:nmusto01@medlib.iaims.georgetown.edu]Sent:  Wednesday, April 24, 1996 8:53 PMTo:  wilcox@xroads.comSubject:  density measurements and immage  reversalI am new to IT and have been playing around with it for a short while. Iam interested in using it to make density measurement of scanned inimmages of electrophoresis gels. I have read past postings regardingthis topic and find I need to use a "plug-in". Is there any move a footto product such an item. For us "programming impared" we are clue=3Dlessas to how to do this. Such density measurements are at the core ofquantitative biology, so I suspect someone must have worked it out.anybody???Simple density measurements are available using the density calibration =feature on the Settings menu.  We are in the process of designing gel =analysis plug-ins for ImageTool.  We hope to have them done in the =relatively near future - we recognize this as one of the most important =missing features of the program.Second question: I cannot figure out how to invert the values of animage, that is to make the black areas 256 and the white 0. Any helphere??You can to this on an image-by-image basis using the contrast control, =or by applying a color table to the image.  The file Inverse.pal, which =is shipped with the installation, will do this.  Note that this will =change the appearance of the images, there is no feature that will cause =ImageTool to display the numbers inverted, although this will likely be =added in the next release.Don------------------------------Date: Sat, 4 May 1996 08:48:10 -0400 (EDT)From: Gregory Forbes To: it-list@sparky.uthscsa.eduSubject: measuring lesion area on leavesMessage-ID: <199605041248.IAA27627@postoffice.mail.cornell.edu>We would like to use IT to measure leaf green area and diseased area.  Wenow have some color images digitized and have measured both the green anddiseased areas by tracing the perimeters, but we would like to know how todo this by separating colors or gray scales.  The images we have digitizedare as follows: width 640, height 480 and BPP = 8.  I would appreciate anysuggestions on the best way to go about this.Thanks,Greg ForbesGreg Forbes,   plant pathologist,  International Potato Center (CIP)Quito, Ecuador                                                    Email:  gaf2@cornell.edu                                                                         CURRENTLY:   Dept. Plant Pathology, Cornell University, 334 Plant Science Bldg.   Ithaca, NY  14853Fax:  +1(607)2554471   Tel:   +1(607)2553188------------------------------Date: Tue, 7 May 1996 08:56:05 -0400From: dcm@image.bio.bnl.gov (Denise Monteleone)To: IT-LIST@sparky.uthscsa.eduSubject: NT/ImageTool running slowlyMessage-ID: <199605071256.IAA23581@image.bio.bnl.gov>I installed ImageTool on my 3.51 NT pentium 90 pc with 16mb ram, and it runs very slowly. What's wrong?------------------------------Date: Wed, 8 May 1996 09:33:58 -0400From: Gilles Leduc To: it-list@sparky.uthscsa.eduSubject: problem to capture imageMessage-ID: <96May8.083803edt.4674@janus.ochin.on.ca>Hi, we've been trying to setup Image Tools to work on a PC. I am new at this and until now I haven't been able to capture any image. I am using aColor video capture board Assy 200014. This is an older board (1990)and I haven't been able to get any information on its compatibility withWindows. Maybe you know something about this video capture board orcan recommend some low cost board already tested on Image Tools.Thanks.Gilles LeducRoyal Ottawa Health Care Groupgleduc@rohcg.on.ca------------------------------Date: Thu, 9 May 1996 22:32:45 -0700 (PDT)From: Jeff Eriksen To: it-list@sparky.uthscsa.eduSubject: Re: IT 1.23Message-ID: <199605100532.WAA17976@desiree.teleport.com>At 12:32 PM 4/27/96 +0600, you wrote:>I finally got a chance to try version 1.23. I am running IT on the Pentium>attached to my SEM. The TIFF images are acquired using Quartz PCI, usually>at 1024 X 840 X 8 bit. When I tried to analyse these images in IT1.23, I>got a "GDI failure" and fatal crash on "Object Analysis". If I re-size the>images in PCI to 640 X 525, then IT does the whole job flawlessly. This>project is sizing polystyrene spheres, 1 to 2 microns diameter.>My suggestion for IT in a future edition is some method to manually "cut">and "join" particles in the binary image, when your best efforts at>separating the touching particles with "Open", "Close", "Erosion" and>"Dilation" just won't quite do it. In my sample, the spheres sometimes>won't separate, and the objects that represent two or more spheres touching>must be rejected. A simple pointer that changed a pixel to the other value,>0 or 1, would do very nicely to break the connection.>Thank you for an excellent program.>Regards,>Mary>>Mary MagerSounds like a job for watershed.  It can separate particles much better thansimple dilation/erosion.  I vote to include watershed analysis in a futureversion.  I can provide references.-JeffJeff Eriksen                             *   K. Jeffrey Eriksen, Ph.D.Scientific Systems Engineer              *   ScientistEEG Dept, T340                           *   Principal InvestigatorLegacy Good Samaritan Hospital           *   Electrical Geodesics1015 NW 22nd Ave                         *   1811 Garden Ave, Suite 104Portland, OR 97210                       *   Eugene, OR  97403(503) 413-7886 voice, 237-5568 pager     +   (541) 687-7962 voice(503) 413-6272 fax                       +   (541) 687-7963 faxJEriksen@teleport.com                    *   JEriksen@egi.com;http://www.egi.com/~egi/------------------------------Date: Fri, 10 May 1996 09:01:13 -0500 (CDT)From: "S. Brent Dove" To: IT List Subject: Separation of objectsMessage-ID: <01I4J9WE5P90009A1M@uthscsa.edu>Hello,Recently several users have indicated problems associated with the separation of joined objects for object anlysis.  Under some circumstances traditional dilation/erosion/open/close method do not work.  Some have suggested using manual pixel modification to separate object.It has also been suggested to use a watershed segmentation>Sounds like a job for watershed.  It can separate particles much better than>simple dilation/erosion.  I vote to include watershed analysis in a future>version.  I can provide references.Can anyone suggest a place to obtain specific implementation of the Watershed algorithm either a place to get actual source code or a detailed reference on the algorithm so we can include it in the next release of ImageTool.Thanks for the help.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------------------------------End of IT-LIST Digest 20