IT-LIST Digest 15Topics covered in this issue include:  1) analysis/stacks	by "Laury Chaerle"   2) RE: analysis/stacks	by Don Wilcox   3) 3-color macro	by Hal Hawkins   4) 	by "S. Brent Dove"   5) IT version 1.23	by Christopher Spry   6) RE: IT version 1.23	by "Coppola, Richard"   7) IT Zip version 1.23	by "S. Brent Dove"   8) Stacks Show All Bug - Version 1.23	by fritz@tcpcs2.dnet.etn.com  9) Re: Stacks Show All Bug - Version 1.23	by MARIETRG@SLUVCA.SLU.EDU 10) tif	by "Heberto Ghezzo" ----------------------------------------------------------------------Date: Tue, 19 Mar 96 23:38:50 METFrom: "Laury Chaerle" To: Subject: analysis/stacksMessage-ID: 1.Is there with the current version 1.2 of the program a possibility to manually draw more than one area? Or can it be solved with a plug-in?As stated by someone before, it would be nice if area's & points could be saved and reused on later occasions. In addition a possibility to 'group and move' several areas/points (alike function in popular drawing programs)could be interesting for analysis of moving targets.2. "All of ImageTool's processing and analysis functions are available on the individual images in the stack".After drawing an area on the first image, is it possible to use this area to measure the same region in the subsequent images of the stack, using a plug-in? Is the association between the stack window and the area kept when the next image is selected?  The help-text mentions for the find-objects function :"The objects are maintained in association with the image window for as long as the image is not changed.  This allows further analysis based upon the objects by analysis plug-ins"Best Regards,Laury ChaerleLab of Genetics, University of Gent, Belgium------------------------------Date: Tue, 19 Mar 1996 15:50:03 -0700From: Don Wilcox To: 'ImageTool List Server' Subject: RE: analysis/stacksMessage-ID: <01BB1690.BF144920@slip2.xroads.com>Hello:----------From:  Laury Chaerle[SMTP:lacha@genwet1.rug.ac.be]Sent:  Tuesday, March 19, 1996 3:24 AMTo:  wilcox@xroads.comSubject:  analysis/stacks1.Is there with the current version 1.2 of the program a possibility to=20manually draw more than one area?=20It is not possible to draw more than one area at a time.  Of course, you =can draw the areas sequentially, but I suspect this is not what you =need.Or can it be solved with a plug-in?Anything (almost) can be solved with a plug-in, this included.As stated by someone before, it would be nice if area's & points could =be=20saved and reused on later occasions.=20It would be nice.  This is currently on the "I'm thinking about how it =would be best to add it to ImageTool" list.  This list bears no =relationship to any likelihood that the feature would be implemented.  =It is equally possible that I would decide that it belongs with some =other pending feature, and so it gets postponed until the feature is =implemented as it is possible that I would wake up one morning, decide =that it stands alone as a feature and is very easy to implement, and so =I toss it in in a spare moment.In addition a possibility to 'group and=20move' several areas/points (alike function in popular drawing programs)could be interesting for analysis of moving targets.I've never seen this idea presented before.  It could be done using a =stack plug-in.  You would need to get the original aois from the user, =and then in successive images in the stack have the user indicate =somehow how much the objects have moved.2. "All of ImageTool's processing and analysis functions are available =on the=20individual images in the stack".Quoting me, huh?  That's a dirty trick!After drawing an area on the first image, is it possible to use this =area to=20measure the same region in the subsequent images of the stack, using a=20plug-in? Is the association between the stack window and the area kept =when=20the next image is selected?  The help-text mentions for the find-objects =function :"The objects are maintained in association with the image window for as =long=20as the image is not changed.  This allows further analysis based upon =the=20objects by analysis plug-ins"AOIs belong to individual images in a stack.  I should mention that I =added stacks without a real good feeling for the types of things one =might want from them.  It is clear that the feature set for stacks will =be moving a bit over the next couple of releases as I tighten it up to =match the actual needs of users.  Be assured that some form of this =feature will be added in the relatively near future (1-2 releases).  =Probably the biggest problem with having AOIs persist between images in =a stack is that there is no mechanism in ImageTool to measure an =existing AOI.  A more likely scenario is that I add an option to measure =the same area in all images in the stack.Best Regards,Laury ChaerleLab of Genetics, University of Gent, BelgiumThank you for your interest in ImageTool,Don------------------------------Date: Tue, 26 Mar 1996 12:56:22 -0500 (CDT)From: Hal Hawkins To: it-list@sparky.uthscsa.eduSubject: 3-color macroMessage-ID: <01I2SN0DF4N0002PUA@BEACH.UTMB.EDU>Having just talked to the Oncor imaging guy at pathology meetings, I wonderwhether the macro which separates 24-bit color images into three 8-bitmonochrome image planes can work in reverse or another macro can do this, i.e: Is there a way to store three successive B&W images using R, G and B filtersand subsequently combine them to make a 24-bit color image?  Of course sucha utility would also allow for input of multiple narrow-band color inputs which might represent different fluophores, thus an 8-color image.  Perhapsthat would best be kept in a stack, but the option to make 3-color false-color images of IR or UV "colors" would be very nice.------------------------------Date: Thu, 28 Mar 1996 07:02:37 -0600 (CST)From: "S. Brent Dove" To: IT Announce ,Message-ID: <01I2V38HF7EO00FAZ6@uthscsa.edu>Hello ImageTool Users,This is to announce the release of UTHSCSA ImageTool version 1.23This upgrade fixes some of the bugs reported in version 1.20 and some added new features.  In the conversion of the application to handle gray scale images that were 16 bits deep, many changes were made to features within the application.  Several errors were discovered in the density calibration which caused to program to crash.  This update fixes all known bugs.In addition several suggestions have been incorporated into this new version.  It is now possible to find objects and then manually select the objects that you wish to be analyzed. The Data Translation driver has been improved to make image acquisition faster, we have also added the ability to automatically capture images over a specific period of time. We have also added the ability to apply a specific processing function to all images in a stack.We are currently working on a display module for the National Library of Medicine Visible Human project, a DICOM 3.0 file filter and a more complete gel analysis plugin.Thanks for all your suggestions and comments.  Keep them comming and we will try to make UTHSCSA ImageTool the most complete imaging software available.Remember you can get UTHSCSA ImageTool version 1.23 from our web site athttp://ddsdx.uthscsa.eduOr the software and source code from our ftp site, the address is;ftp://maxrad6.uthscsa.eduI hope that UTHSCSA ImageTool will help you in your research effort.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: Thu, 28 Mar 1996 14:17:50 gmtFrom: Christopher Spry To: it-list@sparky.uthscsa.eduSubject: IT version 1.23Message-ID: > This is to announce the release of UTHSCSA ImageTool version 1.23There is no 'ver_1_23' directory on the ftp server maxrad6 in /ftp/pub/it. Where should I look for the new version?Christopher Spry------------------------------Date: Thu, 28 Mar 96 09:52:00 estFrom: "Coppola, Richard" To: it-list Subject: RE: IT version 1.23Message-ID: <315AA7B1@SMTP2.mm.hub.nih.gov>re the new version:     dll.zip is okay but it.zip is corrupt, I have been unable to get pkunzip to be happy with it.     Richard Coppola------------------------------Date: Thu, 28 Mar 1996 13:02:29 -0600 (CST)From: "S. Brent Dove" To: IT Announce ,Subject: IT Zip version 1.23Message-ID: <01I2VFSN8O2W00FAZ6@uthscsa.edu>Hello IT users,A funny thing happened on the way to the ftp server.  It seems that the IT.ZIP file was corrupted and could not be unzipped.  I apologize for the problem, I took the file off the server and have tested the new IT.ZIP file which is presently on the server.Please download the new version which is in the root of the ftp/pub/it subdirectory. It is reeeeeaally OK.  We are currently upgrading our NT server to handle the increased load for ImageTool.  We are also currently working out several mirror sites both in the US and overseas which should help getting the latest version of UTHSCSA ImageTool.Well 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, 29 Mar 1996 09:28:18 -0500From: fritz@tcpcs2.dnet.etn.comTo: "IT-LIST@sparky.uthscsa.edu"@WHQST1.dnet.etn.comSubject: Stacks Show All Bug - Version 1.23Message-ID: <9603291428.AA07366@etn.com>***********************************************************************OBSERVATION REPORTProject Classification: Computer Aided Tools - Vendor / User SupportObservation Report Target: UTHSCSA Image ToolObservation Synopsis: Fatal program error using Stacks / Show All command.Observation Details: Following the creation of a stack and selection of the command Stacks / Show All, the stack window did not scan through the images of the stack but displayed an incrementing Image X / Y.  This was followed by loss of current window task controls with keyboard and mouse, followed by a fatal error and task termination.Observation Repeatable: Yes; 3 of 3 times.Software Revision: UTHSCSA Image Tool Version 1.23Operating System: Windows NT Version 3.51 Build 1057: Service Pack 3Hardware Platform:  Gateway 2000 P5/90;   Processor x86 Family Model 2 Stepping 1;3.2G Hard Drive; 64Meg Ram;  ATI Mach64 Graphics controller 1024 X 768 X 64k colors Date of observation: 3/29/96Observer: Todd W. Fritz / Eaton Corporation (616) 342-3368**********************************************************************Symptom: Using Stack Show All on a constructed stack causes a fault and fatal error in Windows NT.Procedure: 1) Load a 24 bit image file.2) Seperate the image into its component RGB using the sequence:Processing / Seperate Colors.3) Create a new stack with Stack / New4) Populate the stack with the three RGB images from step 2 using the sequence:  a. Select image RED  b. Copy the image; Edit / Copy (or CTRL-C)  c. Select the stack  d. Paste the image onto the stack; Edit / Paste (or Ctrl-V)  e. Repeat sequence a. through d. for the images GREEN and BLUE.5) Step through the stack using the left or right arrows.(Observers Note: This is a divergence from the original observation but Ialso noted some distortion in the images at this stage while stepping fromred to blue. The alignment at origin lower left corner assumed to be X=0,Y=0 is fine for all three color images but there is distortion in my imagein the upper left and upper right corners furthest from the origin.  I don't notice any distortion in the original image, only after the processing and stack creation.  The image is a 24 bit capture from a Hitatchi VK-C370 CCD camera using a Hauppauge Win/TV Celebrity card in S-Video mode.  I will be investigating this further to make sure there is no distortion generated from the digital signal processors of my video system.) 6) Select the command: Stack / Show All. a. Status Line: Open new images windows each showing a different image    from the stack. b. Stack window title displays stack name (new) and an incrementing count     in the format ( X / X+1 ).  This count countinued to increase until it     reached ( 220 / 221 ) at which time the all activity on the system     stopped.  c. The following dialog appeared: ObjectWindows Exception - GDI Failure.  d. At this point, the program abnormally terminated.7) The following dialogs were displayed after selecting OK on the GDI failure dialog:  a. Dr. Watson 32 Bit Log: Access violation.  b. System alert: Low virtual memory (Currently at 75 - 125 Meg Bytes).Respectively Submitted,Todd FritzPrincipal Engineer, ElectronicsFRITZ@TCPCS2.DNET.ETN.COM(616) 342-3368Eaton CorporationTruck Components Operations North AmericaAutomation Business Unit13100 E. Michigan Ave.Galesburg, Michigan 49052Eaton Corporation Disclaimer For Employee Internet Usage"The contents of this message are mine solely and do not reflect the views of Eaton Corporation. Eaton has not reviewed nor appproved of this message.I speak for myself. I am not authorized to speak for Eaton."------------------------------Date: Fri, 29 Mar 1996 12:43:43 -0600 (CST)From: MARIETRG@SLUVCA.SLU.EDUTo: it-list@sparky.uthscsa.eduSubject: Re: Stacks Show All Bug - Version 1.23Message-ID: <01I2WTEIKF3MBHIJ48@SLUVCA.SLU.EDU> Hey Todd W. Fritz of the Eaton Coprporation,I noticed you said you were running NT 3.51 Service Pack 3.Service Pack 4 is out...  Try That.Bob Mariettamarietrg@sluvca.slu.edu------------------------------Date:          Fri, 29 Mar 1996 14:06:51 EST5EDTFrom: "Heberto Ghezzo" To: it-list@sparky.uthscsa.eduSubject: tifMessage-ID: <199603291910.OAA29947@sirocco.CC.McGill.CA>I just dowloaded version 1.23. I am sorry but 'it' does not like my file inm2.tif. and send me to import file.  when I open the file with Hi-Jack it reports that the file is TIFF, 320 x 240 3 bits per sample and opens it with no problems.The TIFF files that are 8 bits palette are open by 'it' with no problem but then I can not turn them to gray scale to identify spots etc.Am I doing something wrong?.R. Heberto Ghezzo  Ph.D.Meakins-Christie LabsMcGill UniversityMontreal - Canadaheberto@meakins.lan.mcgill.ca------------------------------End of IT-LIST Digest 15