IT-LIST Digest 7Topics covered in this issue include:  1) Re: density measurements	by "S. Brent Dove"   2) Re: Image Tool errors	by "S. Brent Dove"   3) Re: Importing Files	by "S. Brent Dove"   4) Re: Thresholding images	by "S. Brent Dove"   5) plug ins and file filters	by ben   6) Re: plug ins and file filters	by read@boulder.nist.gov (David T. Read)  7) Importing Meridian Image Files	by read@boulder.nist.gov (David T. Read)  8) printing problem	by Przemko Tylzanowski   9) Re: printing problem	by Peter.Stalmans@med.kuleuven.ac.be (Peter Stalmans) 10) Re: Thresholding images	by "Heberto Ghezzo"  11) RE: Thresholding images	by Don Wilcox  12) Frame Grabber or Scanner Support	by bell@upanet.uleth.ca (Craig Bell)----------------------------------------------------------------------Date: Tue, 06 Feb 1996 08:05:30 -0600 (CST)From: "S. Brent Dove" To: IT List Subject: Re: density measurementsMessage-ID: <01I0VWKSC4EA002EDS@uthscsa.edu>Hello IT Users,>  Is there a way that I can measure the density (intensity of pixels) in>an area rather than just a line?  One option, I suppose would be to take>a rectangle and average the intensity across the width and do a density>profile with a line across the averages.  Is this possible?No, ImageTool does not provide a method for doing this.  You could write a plugin to perform such an analysis.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: Tue, 06 Feb 1996 08:05:36 -0600 (CST)From: "S. Brent Dove" To: IT List Subject: Re: Image Tool errorsMessage-ID: <01I0VWKVYBWO002EDS@uthscsa.edu>>It seems that I am not the only one getting the error below when I try to>run Image Tool version 1.1 on Windows 95.> When I try to analyze a jpeg image, it counts the objects satisfactorily>but when I try>to do an Object Analysis the program crashes with the following message:>>        IT caused an exception 10H in module UTILIB31.DLL at>                0137:006d345b>>Once this error is cleared and I quit the program I get the error:>        IT caused an exception C0000026H in Module KERNEL32.DLL at>                0137:bffb87c0>>Any idea why this is occuring?The problem occurs when IT attempts to compute the histogram statistics for an object that is exactly one pixel in size.  The bug has been fixed and will not occur in version 1.2.  In the meantime, you can eliminate the problem by changing the object size theshold in the Find Objects tab of the settings dialog to be greater than 1.Sorry for the problems.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: Tue, 06 Feb 1996 08:05:42 -0600 (CST)From: "S. Brent Dove" To: IT List Subject: Re: Importing FilesMessage-ID: <01I0VWL0H83M002EDS@uthscsa.edu>>The old Image Tool used to open an "importing window" when trying to open a>binary file.  I can't seem to get the new version to do this.  Can anyone>tell me what I am doing wrong?It could be that you do not have an up-to-date version of the binary file filter plug-in.  You can try downloading a new copy of the file ~binfltr.dll from the ftp site.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: Tue, 06 Feb 1996 08:05:47 -0600 (CST)From: "S. Brent Dove" To: IT List Subject: Re: Thresholding imagesMessage-ID: <01I0VWL4FHMG002EDS@uthscsa.edu>>I'm having problems thresholding scanned in PCX type colour images i.e. I>can't use the  threshold, contrast and erode & dilate routines on these>images.   Any ideas why  this is or am I missing something dead simple?>(Interestingly if I use 'Find Objects' it goes into the thresholding routine>ok, any ideas?)IT does not provide many analysis features for color images.  The fact that Find Objects is not diabled is a bug that will be fixed in version 1.2.  There is a general feeling here that some additional color support may be useful in the future, but our current emphasis in on gray scale imaging.  It would be possible to write a plug-in that converted the color image to grayscale (perhaps using HSV values) and then IT could analyze the resulting image, but the analysis would not be of the original color data.  If you really need color analysis, you are currently stuck with commercial tools such as Photoshop.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: Tue, 6 Feb 1996 10:20:17 -0500 (EST)From: ben To: it-list@sparky.uthscsa.eduSubject: plug ins and file filtersMessage-ID: I was trying to get the file filters and contour extraction plug ins; however I was not able to find the plug in extraction.  Also was was not able to change directories into the file filters directory.  Any thoughts on this?- ben------------------------------Date: Tue, 06 Feb 1996 10:49:15 -0700From: read@boulder.nist.gov (David T. Read)To: it-list@sparky.uthscsa.eduSubject: Re: plug ins and file filtersMessage-ID: <199602061756.KAA10571@arc1.mrd.bldrdoc.gov>>>I was trying to get the file filters and contour extraction plug ins; >however I was not able to find the plug in extraction.  Also was was not >able to change directories into the file filters directory.  Any thoughts >on this?>>- benUse double quotes .....  "file filters"   .I haven't gotten them to work, but I did manage to download.Informal communication from:     David T. Read     Materials Reliability Division, 853     National Institute of Standards and Technology     325 Broadway     Boulder, Colorado 80303     Phone:  303 497 3853     Fax:    303 497 5030------------------------------Date: Tue, 06 Feb 1996 10:59:59 -0700From: read@boulder.nist.gov (David T. Read)To: it-list@sparky.uthscsa.eduSubject: Importing Meridian Image FilesMessage-ID: <199602061807.LAA10610@arc1.mrd.bldrdoc.gov>It has been stated that>...the>binary file filter provided by IT should be adequate for your purposes.  >It>allows you to specify the byte offset of the data, along with the size>(width, height, bit depth) of the data itself.  If your images are 8 bit>gray scale or 24 bit color, then this should work for you.  Simply make >sure>that the file ~binfltr.dll is in the "File Filters" directory (if not, you>can download it from maxrad6), and then select the image files from the >open>dialog box.This didn't work for me.  I got the ~binfltr.dll, created the File Filtersdirectory, and put the ~binfltr.dll into it.  IT seemed to recognize the dllbecause it added a choice for "binary files" in the open dialog.>  You will be presented with a dialog in which you can specify>the image information.  Note that if every image is exactly the same, When I tried to use it, it did not present me with the binary filespecification dialog and then was unable to read the file.  If anyone knowswhat might be amiss with my installation, please advise.then>you will never need to re-enter this data, as IT will remember it across>invokations.  If you have access to a copy of Borland C++ and have or know>someone who can write C++, the IT SDK documentation describes how to >write a>file filter that you could make specific to your application.>>Is it possible to obtain the SDK and source code?I got the source code, and am puzzling my way through it.Revelation number 1:  run implib on utilib31.dll to make utilib31.libProblems:  some apparently missing files that are needed in certain of thedll.  Olgapi.h, included in olframe.h, is the first one, I think.  Namesmight not be exact.Them something in the gamma dll seemed to be missing.Informal communication from:     David T. Read     Materials Reliability Division, 853     National Institute of Standards and Technology     325 Broadway     Boulder, Colorado 80303     Phone:  303 497 3853     Fax:    303 497 5030------------------------------Date: Wed, 7 Feb 1996 08:51:49 +0000 (WET)From: Przemko Tylzanowski To: it-list@sparky.uthscsa.eduSubject: printing problemMessage-ID: Hi!I am very impressedwith IT. Considering that I do not have a Mac (and therefore NIH Image is unavailable to me), IT very nicely addresses some of my need.But...i have a printing problem. I have Pentium 90, 32Mbyte RAM, 1Gb hard drive, WIN95 and a WIN95 network. We have a network printer that works for all computers and with all programs (except WordPerfect, but then who is using that anyway...). Now, >I can anylyse images using IT but I cannot print. I cannot even print the images supplied as a demo. Can anyone tell me what I am doing wrong?ThankXPrzemko------------------------------Date: Wed, 7 Feb 1996 11:22:15 +0100From: Peter.Stalmans@med.kuleuven.ac.be (Peter Stalmans)To: it-list@sparky.uthscsa.eduSubject: Re: printing problemMessage-ID: <199602071022.AA24982@cc5.kuleuven.ac.be>>I can anylyse images using IT but I >cannot print. I cannot even print the images supplied as a demo. Can >anyone tell me what I am doing wrong?You did not mention what printer you are using.In our Win95 network, I can't print on our HP laserjet III because of notenough memory in the printer. Printing on the HP Laserjet 4Mplus (with 6 Mbof memory) on our VINES network causes no problem.I suggest: try printing on a printer with more memory inside.Sincerely,Peter Stalmans, MDPeter.Stalmans@med.kuleuven.ac.beLaboratory of Physiology KULeuvenHerestraat 49B-3000 LeuvenBelgiumtel: +32-16-34 71 46fax: +32-16-34 59 91------------------------------Date:          Wed, 7 Feb 1996 09:19:27 EST5EDTFrom: "Heberto Ghezzo" To: it-list@sparky.uthscsa.eduSubject: Re: Thresholding imagesMessage-ID: <199602071422.JAA00843@sirocco.CC.McGill.CA>Hi, I am new to IT and not very skilled, so far I have been using NIH-IMAGE in a Mac but I want to work in my PC......The problem of not thresholding a color image is a serious one, I will propose to be one of the first to do for version 1.2..What I would want is:  a- change color images, either paletted or 24 bits to gray scale b- manipulate the palette before changing to gray.by manipulate the palette i mean a way to change the colors to a distance. For example in a inmuno stained picture I want to quantize the amount of color corresponding to may stain. I want to indicate in the screen an area of perfect staining and the program to read the palette colors in the area, compute the mean and the then replace the palette with a gray scale indicating distance in 3 color space to that mean, thus in the transformed scale 'black' will indicate the same color as the stain, 'dark gray' very close color and 'white' a completely opposite color. Thresholding this image I can  obtain the total area stained ( amount) or count the number of cells stained, etc.Also I did not find a way to indicate manually what is an 'object' to measure, for example I am opbserving lung tissue, I want to point to an alveoly or alveolar duct, mark them and have the program give me the perimeter, area, diameters, etc.Well, this is my wish list, is anything of that already done by somebody whom can contribute their plugs-in?ThanksR. Heberto Ghezzo Ph.D.Meakins-Christie LabsMcGill University Canada------------------------------Date: Thu, 8 Feb 1996 08:31:56 -0700From: Don Wilcox To: 'ImageTool List Server' Subject: RE: Thresholding imagesMessage-ID: <01BAF603.42E74EE0@slip17.xroads.com>a- change color images, either paletted or 24 bits to gray scale b- manipulate the palette before changing to gray.by manipulate the palette i mean a way to change the colors to a=20distance. For example in a inmuno stained picture I want to quantize=20the amount of color corresponding to may stain. I want to indicate in=20the screen an area of perfect staining and the program to read the=20palette colors in the area, compute the mean and the then replace the=20palette with a gray scale indicating distance in 3 color space to=20that mean, thus in the transformed scale 'black' will indicate the=20same color as the stain, 'dark gray' very close color and 'white' a=20completely opposite color. Thresholding this image I can  obtain the=20total area stained ( amount) or count the number of cells stained,=20etc.This is a good idea.  We have been considering ways in which to handle =color thresholding, and this is certainly a very good method for doing =so.  Unfortunately, we will not get this feature into version 1.2 of =ImageTool, as we are running up against a hard deadline.  You understand =that this could be done as a plug-in if you were willing to have =analysis done on the gray scale image, instead of on the color image.  =The plug-in would perform the color-to-distance mapping and produce the =gray scale image.  If you need to be able to analyze the color image, =then the feature needs to be added to IT, since the plug-in cannot add =objects to an existing image (this will be changed in a later revision =of the plug-in interface).Also I did not find a way to indicate manually what is an 'object' to=20measure, for example I am opbserving lung tissue, I want to point to=20an alveoly or alveolar duct, mark them and have the program give me=20the perimeter, area, diameters, etc.This feature will be added to version 1.2 of ImageTool.Well, this is my wish list, is anything of that already done by=20somebody whom can contribute their plugs-in?Thank you for your interest in IT, and for your suggestions.  I hope =------------------------------Date: Sat, 10 Feb 1996 20:56:29 -0700From: bell@upanet.uleth.ca (Craig Bell)To: IT-LIST@sparky.uthscsa.eduSubject: Frame Grabber or Scanner SupportMessage-ID: <9602110350.AA16763@sparky.uthscsa.edu>I need to know if the next version of Image Tool (The Windows 95 version!)will have support for Frame grabbers and Twain Devices.  In addition, Iwould like to know if it is possible to get Image Tool to use the framegrabber that I already use (Coreco TCX frame grabber).  Image Tool is veryfast and I would love to use it with my current applications and equipment.However, I do not know how to acquire images (short of loading files intothe program). Is it possible to have the macros "remember" what parameters you set forthresholding processes?  It's hard to automate our applications when we haveto keep telling the program how to threshold the image.  With respect to color imaging, is there a "convert-to-greyscale" option Ihave not seen yet? I can't threshold anything that isn't a greyscale but Ihaven't found a consistent way to create the greyscale! If anyone can provide assistance with these questions, I would be verygrateful.  Thanks for creating a very useful (and fast!) image analysis product, and Ianticipate using the next version later on this month.---Craig Bell            e-mail: BELL@upanet.uleth.caPublic Access InternetThe University of Lethbridge------------------------------End of IT-LIST Digest 7***********************