IT-LIST Digest 37Topics covered in this issue include:  1) Re: Beginner question - densitometry	by golfredo@ciens.ula.ve (CATALANI GOLFREDO)  2) TIff and BMP formats: help please	by "BRYAN J. CROSBY"   3) Re: TIff and BMP formats: help please	by Robert Smith   4) Re: TIff and BMP formats: help please	by dcm@image.bio.bnl.gov (Denise Monteleone)  5) Re: Stacks -> avi?	by "Don Wilcox"   6) Re: TWIAN acquire	by "Don Wilcox"   7) Re: Beginner question - densitometry	by "Don Wilcox"   8) Re: TWIAN acquire	by James Zheng   9) Re: TWAiN acquire	by "Don Wilcox"  10) memory problem and morphology	by "Dr. Bin Yu"  11) Re: TIff and BMP formats: help please	by Peter Stalmans  12) Re: memory problem and morphology	by "Don Wilcox"  13) Re: memory problem and morphology	by "Dr. Bin Yu" ----------------------------------------------------------------------Date: Wed, 14 Aug 96 09:55:36-040From: golfredo@ciens.ula.ve (CATALANI GOLFREDO)To: it-list@sparky.uthscsa.eduCc: golfredo@ciens.ula.veSubject: Re: Beginner question - densitometryMessage-ID: <9608141355.AA12673@tenar>	I need too know it make DENSITOGRAM'S to gel's of PAGE & IEF,	How do I to respect....	please!!!!			Golfredo Catalani			Lab. Fermentaciones ULA Merida  Venezuelathank's------------------------------Date: Wed, 14 Aug 1996 18:04:19 GMTFrom: "BRYAN J. CROSBY" To: it-list@sparky.uthscsa.eduSubject: TIff and BMP formats: help pleaseMessage-ID: <9401FF7662@phys-irc.novell.leeds.ac.uk>Please can someone help me quickly,my time is running out at presentI am writing an app. which is meant to write files of images in formats which can be read by another app such as IT. Could someone quickly point me in the right direction for either a web site with info on Bitmap, TIF, GIF etc file formats or a book on the subject or bothyour sincerely Bryan J. CrosbyIRC in Polymer Science and TechnologyUniversity of LeedsLeeds LS2 9JTPh :Lab & Office :+44(0)113 2333 904    Fax          :+44(0)113 2333 846Email phybjc@gps.leeds.ac.uk   or B.J.Crosby@leeds.ac.uk------------------------------Date: Wed, 14 Aug 1996 13:20:20 -0400From: Robert Smith To: it-list@sparky.uthscsa.eduCc: B.J.Crosby@leeds.ac.ukSubject: Re: TIff and BMP formats: help pleaseMessage-ID: <1.5.4.32.19960814172020.0067d86c@curtech.com>At 12:05 PM 8/14/96 +0600, you wrote: Could someone quickly point me in the right direction for >either a web site with info on Bitmap, TIF, GIF etc file formats >or a book on the subject Bryan:   You can get format info and conversion code in C from:                Bitmapped Graphics    and                Supercharged Bitmap Graphics                by Steve Rimmer                Windcrest/McGrawHill        also                Programming for Graphics Files in C and C++                John Levine                WileyGood LuckBob             .  Robert A. Smith, Ph.D.  _____    .    Vision Systems' Analyst |     |<.      Current Technology, Inc. |_____|   .    (603) 868-2270     ^       .  ras@curtech.com    / \   /   \------------------------------Date: Wed, 14 Aug 1996 13:23:58 -0400From: dcm@image.bio.bnl.gov (Denise Monteleone)To: it-list@sparky.uthscsa.eduSubject: Re: TIff and BMP formats: help pleaseMessage-ID: <199608141723.NAA12558@image.bio.bnl.gov.>There is a book called Graphics File Formats (reference and guide) byC. Wayne Brown and Barry J. Shepherd. You can order it from McGraw Hill pub.------------------------------Date: Sat, 17 Aug 1996 06:31:49 -0700From: "Don Wilcox" To: Subject: Re: Stacks -> avi?Message-ID: <199608171408.HAA24767@dogbert.xroads.com>----------> From: Len Cleary > To: wilcox@xroads.com> Subject: Stacks -> avi?> Date: Monday, August 12, 1996 3:52 AM> > Hello,> > Can anyone suggest a way to convert an IT stack to an avi movie? I don't> think our machines have enough horsepower (100 MHz pentiums, 16 MB RAM)to> use Imagetool as a Netscape viewer.> > Cheers,> Len Cleary, Ph.D.> Dept. of Neurobiology & Anatomy> Univ. Texas Houston Medical SchoolThis could be done by writing a plug-in for ImageTool.  This, of course,requires someone with some programming expertise.  If you have someone whocould write a program that converted a saved stack to an avi file, then thatperson could write an ImageTool plug-in.  A developer's kit is available onthe ftp server.  The SDK contains the source code for ImageTool and all ofthe standard pug-ins that we ship.  Support for developers is provided onthis forum.Don------------------------------Date: Sat, 17 Aug 1996 06:45:15 -0700From: "Don Wilcox" To: Subject: Re: TWIAN acquireMessage-ID: <199608171408.HAA24770@dogbert.xroads.com>----------> From: James Zheng > To: wilcox@xroads.com> Subject: TWIAN acquire> Date: Monday, August 12, 1996 11:06 PM> > Hello,> > I understand that IT 1.25 is to be released soon (August 24?).  Can you > guys modify the program so that TWAIN Acquire will not AUTOMATICALLY > close after acquiring an image.  I am using TWAIN interface to control > an image processor (Hamamatsu Argus-20) and I would like to leave the > TWAIN acquire open until I finish all the work.  Thanks.Let me think about that.> As for writing customer plug-in, how do I deal with 16-bit images (i.e. > from cooled CCD).  ITSDK mentions that the acquire plug-in should return > a DIB, but I have no idea about 16-bit grayscale images.  I plan to > write a IT plug-in for Photometrics PXL series of CCDs. There is a section at the beginning of the SDK manual on 16 bit DIBs. Windows itself added support for 16 bit color DIBs with the release ofWin95.  What I did to provide support for 16 bit grayscale DIBs was toabscond with one of the fields and use it for my own purposes.  When youcreate a 16 (or 32) bit DIB, you set the compression field of the BITMAPINFOto BI_BITFIELDS, which tells Windows that the three longs after theBITMAPINFO are flag values that tell where the red, green, and blue colorbits can be found in the pixel values.  To create a 16 bit DIB and letImageTool know that it is grayscale, simply set all three flag values to thesame value.  This also allows you to tell ImageTool what the effectivegrayscale value range is.  For example, to create a 16 bit DIB with datavalues that are actually 12 bits deep (instead of 16), you would set theflag words to 0x00000fff.  By telling ImageTool the actual data range, youwill get better precision on histograms and other grayscale measurements. For an example of how to create and manipulate a 16 bit DIB, you will wantto look at the source code for the Tiff reader.  There is also goodinformation available from Microsoft, the smaple program ShowDib at the ftpsite does much of the bit mask manipulation.  If you have any morequestions, feel free to ask.Don------------------------------Date: Sat, 17 Aug 1996 06:47:47 -0700From: "Don Wilcox" To: Subject: Re: Beginner question - densitometryMessage-ID: <199608171408.HAA24773@dogbert.xroads.com>----------> From: Denise Monteleone > Subject: Re: Beginner question - densitometry> Date: Tuesday, August 13, 1996 7:25 PM> > Brent,> > 	I am really glad that you are adding more features for electrophoresis> gel analysis. We do alot of them and also sequencing gels. So thanks, andkeep> thoses new features coming.> > Brent did not mention this, but we are designing plug-ins for a wide varietyof gel analysis problems.  The process is fairly straightforward, but doingit right requires a lot of user interface, which takes a lot of time.  As wefinish such tools, we will make them generally available, but I would nothold my breath.  If I was willing to just slop something together, I couldbe done very soon, but I am not.Don------------------------------Date: Sat, 17 Aug 1996 16:03:10 -0400 (EDT)From: James Zheng To: it-list@sparky.uthscsa.eduSubject: Re: TWIAN acquireMessage-ID: <9608171956.AA16956@sparky.uthscsa.edu>Don,Thank you very much for your reply to my e-mail concerning TWAIN acquireinterface.  I just want to provide you more information here.  Unlikenormal scanner's TWAIN plugins, the TWAIN plugin I use can do imageacquisition as well as direct control of the image processor.  I normally use it to directly control the image processor and acquire several images.  It is kind of frustruting right now since the plug-in closes after acquiring a single image.  The plugin has a "quit" button for closing down the interface.  The same plug-in works on Adobe Photoshop 3.04 without the problem.  However, as we all know, ImageTool is a much better problem for analysis.  James------------------------------Date: Sat, 17 Aug 1996 17:47:12 -0700From: "Don Wilcox" To: Subject: Re: TWAiN acquireMessage-ID: <199608180055.RAA06506@dogbert.xroads.com>> > Don,> > Thank you very much for your reply to my e-mail concerning TWAIN acquire> interface.  I just want to provide you more information here.  Unlike> normal scanner's TWAIN plugins, the TWAIN plugin I use can do image> acquisition as well as direct control of the image processor.  I normally> use it to directly control the image processor and acquire several > images.  It is kind of frustruting right now since the plug-in closes > after acquiring a single image.  The plugin has a "quit" button for > closing down the interface.  The same plug-in works on Adobe Photoshop > 3.04 without the problem.  I have made a change that will appear in version 1.25 of IT.  Hopefully,this will solve your problem.  If it does not, we can work further then.> However, as we all know, ImageTool is a much > better problem for analysis.  Sucking up to the program author will do you no good :-)Don------------------------------Date: Mon, 19 Aug 1996 20:43:39 -0400From: "Dr. Bin Yu" To: it-list@sparky.uthscsa.eduSubject: memory problem and morphologyMessage-ID: <32190A3B.3F60@cps.msu.edu>Hi,1. How many objects the program can handle? When I run Analysis/FindObject on an 8-bit gray image with a size of 724*941 (681284 bytes), thesystem output a message like "Your system is running low on virtualmemory. Please ...". Actually, our system has 48M memory and 110Mvirtual memory (I tried 400M virtual memory). BTW, with an insuitablethresholding value, there are several thousands objects (noise).2. No morphologic operations in Image Tool 1.23 are active in the menu(grayed). I tried it on both 1-bit and 8-bit binary image.Any assistance and information are appreciated.ThanksBin Yu------------------------------Date: Tue, 20 Aug 1996 13:41:05 +0200From: Peter Stalmans To: it-list@sparky.uthscsa.eduSubject: Re: TIff and BMP formats: help pleaseMessage-ID: <2.2.32.19960820114105.0091af98@popserv.kuleuven.ac.be>>Could someone quickly point me in the right direction for >either a web site with info on Bitmap, TIF, GIF etc file formats >or a book on the subject >or bothFor all information regarding TIFF: see the TIFF homepage:http://icib.igd.fhg.de/icib/it/defacto/company/aldus/read.htmlorhttp://www-mipl.jpl.nasa.gov/~ndr/tiff/index.htmlThese pages contains a 121-page postscript printable file that will supplyyou with all necessary information.Peter Stalmans------------------------------Date: Tue, 20 Aug 1996 14:30:16 -0700From: "Don Wilcox" To: Subject: Re: memory problem and morphologyMessage-ID: <199608202136.OAA07124@dogbert.xroads.com>----------> From: Dr. Bin Yu > To: wilcox@xroads.com> Subject: memory problem and morphology> Date: Monday, August 19, 1996 7:16 AM> > Hi,> > 1. How many objects the program can handle? When I run Analysis/Find> Object on an 8-bit gray image with a size of 724*941 (681284 bytes), the> system output a message like "Your system is running low on virtual> memory. Please ...". Actually, our system has 48M memory and 110M> virtual memory (I tried 400M virtual memory). BTW, with an insuitable> thresholding value, there are several thousands objects (noise).> There is an effective limit of about 1000 objects in IT running under Win95with 32 MB of RAM, and a lot larger limit under NT.  Version 1.25, to bereleased this weekend, will enforce this limit gracefully.> 2. No morphologic operations in Image Tool 1.23 are active in the menu> (grayed). I tried it on both 1-bit and 8-bit binary image.To qualify as binary, the image must contain only two gray levels and iseither 8 or 16 bits deep.  If your images are not passing this test, and youthink they should, let me know quickly so I can check it before Friday. Thanks.Don------------------------------Date: Tue, 20 Aug 1996 18:10:03 -0400From: "Dr. Bin Yu" To: it-list@sparky.uthscsa.eduSubject: Re: memory problem and morphologyMessage-ID: <321A37BB.192@cps.msu.edu>Don Wilcox wrote:> > > 2. No morphologic operations in Image Tool 1.23 are active in the menu> > (grayed). I tried it on both 1-bit and 8-bit binary image.> To qualify as binary, the image must contain only two gray levels and is> either 8 or 16 bits deep.  If your images are not passing this test, and you> think they should, let me know quickly so I can check it before Friday.> Thanks.> > DonThe selected image was binarized from an 8-bit gray image by usingthresholding in IT. I also tried an 1-bit image (which is assumed to beconverted into an 8 bits depth in memory?). it seems that both themdidn't pass the binary test.Thanks,Bin------------------------------End of IT-LIST Digest 37