IT-LIST Digest 1Topics covered in this issue include:  1) How do you do contours?	by ben   2) RE: How do you do contours?	by Don Wilcox   3) RE: How do you do contours?	by ben   4) RE: How do you do contours?	by Don Wilcox   5) 16 bit file formats and plug ins	by ben   6) RE: 16 bit file formats and plug ins	by Don Wilcox   7) Morphometrical analysis of cells on tissue cross-sections	by berquin@fymu.ucl.ac.be (Anne Berquin)  8) RE: Morphometrical analysis of cells on tissue cross-sections	by Don Wilcox ----------------------------------------------------------------------Date: Mon, 6 Nov 1995 14:24:05 -0500 (EST)From: ben To: IT-LIST@sparky.uthscsa.eduSubject: How do you do contours?Message-ID: Is there a way to threshold an image to select just bony areas for example an CT image and then pick out an outlining contour of the thresholded area.  Then save then points of the contours to an ascii file as can be done in NIH Image.- ben=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=Ben Kao           Research Associate Department of Biomedical Engineering4B Post Oak Rd.					Duke UniversityDurham, NC  27705				B218 LSRC(919)382-8265					(919) 660-5153e-mail: bkao@ee.duke.edu=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=------------------------------Date: Tue, 7 Nov 1995 07:22:18 -0700From: Don Wilcox To: "'it-list@sparky.uthscsa.edu'" Subject: RE: How do you do contours?Message-ID: <01BAACE1.EA2321E0@slip28.xroads.com>------ =_NextPart_000_01BAACE1.EA2C49A0Content-Type: text/plain; charset="us-ascii"Content-Transfer-Encoding: quoted-printable----------From: 	ben[SMTP:bkao@ee.duke.edu]Sent: 	Monday, November 06, 1995 12:21 AMTo: 	wilcox@xroads.comSubject: 	How do you do contours?Is there a way to threshold an image to select just bony areas for=20example an CT image and then pick out an outlining contour of the=20thresholded area.  Then save then points of the contours to an ascii =file=20as can be done in NIH Image.I am in the process of adding object identification to IT. The basic =coding is complete, and I am testing the new features.  Our plan is to =release an updated version of IT at or near the end of the month.  There =are no current plans to have the feature you describe.  We will be =supporting extracting measurements from objects (the list is fairly =extensive), and classification of objects based upon these features.  =Would one of these tools meet your needs, or do you specifically need =the contour outlines?Don------------------------------Date: Tue, 7 Nov 1995 09:59:16 -0500 (EST)From: ben To: it-list@sparky.uthscsa.eduSubject: RE: How do you do contours?Message-ID: Don,		I'm not quite sure what you mean by 'extracting measurements from objects' (i.e. what kind of measurements?)  Let me describe an example of what we would like to do and this is what I mean by extracting the contours.  Taking MRI sections of the torso (each section approx. 5 mm apart) we use the thresholding tool to pick out certain organs.  So say for example we set the threshold so that only the liver is selected in that particular MRI slice.  Then using a contouring tool (called the Automatic Outlining Tool or Wand in NIH Image) you can click inside the object area of interest and then spit out the numbers (as in pixel location or distances) into another window.    When you go through and do this for all the slices, we can put them together to generate a 3D shell of each organ which can then be used to generate a mesh which we use in Finite element models.- ben>> Is there a way to threshold an image to select just bony areas for=20>> example an CT image and then pick out an outlining contour of the=20>> thresholded area.  Then save then points of the contours to an ascii =>> file=20>> as can be done in NIH Image.> > I am in the process of adding object identification to IT. The basic => coding is complete, and I am testing the new features.  Our plan is to => release an updated version of IT at or near the end of the month.  There => are no current plans to have the feature you describe.  We will be => supporting extracting measurements from objects (the list is fairly => extensive), and classification of objects based upon these features.  => Would one of these tools meet your needs, or do you specifically need => the contour outlines?> > Don------------------------------Date: Tue, 7 Nov 1995 14:38:08 -0700From: Don Wilcox To: "'it-list@sparky.uthscsa.edu'" Subject: RE: How do you do contours?Message-ID: <01BAAD1E.C6E91C60@slip28.xroads.com>----------From: 	ben[SMTP:bkao@ee.duke.edu]Sent: 	Monday, November 06, 1995 08:00 PMTo: 	wilcox@xroads.comSubject: 	RE: How do you do contours?Don,=09	I'm not quite sure what you mean by 'extracting measurements from=20objects' (i.e. what kind of measurements?)  Let me describe an example =of=20what we would like to do and this is what I mean by extracting the=20contours.  Taking MRI sections of the torso (each section approx. 5 mm=20apart) we use the thresholding tool to pick out certain organs.  So say=20for example we set the threshold so that only the liver is selected in=20that particular MRI slice.  Then using a contouring tool (called the=20Automatic Outlining Tool or Wand in NIH Image) you can click inside the=20object area of interest and then spit out the numbers (as in pixel=20location or distances) into another window.    When you go through and =do=20this for all the slices, we can put them together to generate a 3D shell =of each organ which can then be used to generate a mesh which we use in=20Finite element models.Ben,The new version of IT will do everything up to selecting a specific item =and spitting out the coordinates.  It would be simple to write such a =plug-in.  If you have a programmer, such a project would require not =much time at all (maybe a couple of hours).The new version of IT should be available at the end of the month.Don------------------------------Date: Wed, 8 Nov 1995 11:01:27 -0500 (EST)From: ben To: it-list@sparky.uthscsa.eduSubject: 16 bit file formats and plug insMessage-ID: Does IT support 16 bit unsigned raw integer file formats (with or without, a commonly used raw data format in medical imaging.Also, where can I find information about writing plug ins.Thanks- ben------------------------------Date: Thu, 9 Nov 1995 21:20:44 -0700From: Don Wilcox To: "'it-list@sparky.uthscsa.edu'" Subject: RE: 16 bit file formats and plug insMessage-ID: <01BAAEE9.3EAABDA0@slip9.xroads.com>----------From: 	ben[SMTP:bkao@ee.duke.edu]Sent: 	Tuesday, November 07, 1995 08:57 PMTo: 	wilcox@xroads.comSubject: 	16 bit file formats and plug insDoes IT support 16 bit unsigned raw integer file formats (with or=20without, a commonly used raw data format in medical imaging.Nope.  An acquisition plug-in can be used as a file import, or there are =file filter plug-ins that can be used to open files.  The file filters =are added to the standard open process, so they are transparent.  The =downside is you must be able to recognize your file format, since the =filter is installed in the chain of routines that are called to attempt =to open a new file.Also, where can I find information about writing plug ins.All the docs are on the ftp site, in the file utilibh.zip.  It contains =the source code for IT, for several example plug-ins, and an extensive =help file defining the plug-in interface and the routines and classes =exported from UTILib.Thanks- benDon------------------------------Date: Thu, 23 Nov 1995 09:36:53 +0100From: berquin@fymu.ucl.ac.be (Anne Berquin)To: it-list@sparky.uthscsa.eduSubject: Morphometrical analysis of cells on tissue cross-sectionsMessage-ID: <9511230836.AA00963@lewsun.md.ucl.ac.be>Dear Sirs,I am looking for a method to measure the minimum diameter of cells on tissue(muscle) cross-sections. Would someone have desiged a plug-in or some macrosfor IT that cand perform such a task ?Many thanks in advance,Anne BerquinUniversite Catholique de Louvain, Dept PhysiologyUCL 5540, B-1200 Brussels.Phone 32-2-764.55.28 - Fax. 32-2-764.55.80------------------------------Date: Sat, 25 Nov 1995 11:21:43 -0700From: Don Wilcox To: "'it-list@sparky.uthscsa.edu'" Subject: RE: Morphometrical analysis of cells on tissue cross-sectionsMessage-ID: <01BABB28.457213E0@slip15.xroads.com>----------From: 	Anne Berquin[SMTP:berquin@fymu.ucl.ac.be]Sent: 	Wednesday, November 22, 1995 02:02 PMI am looking for a method to measure the minimum diameter of cells on =tissue(muscle) cross-sections. Would someone have desiged a plug-in or some =macrosfor IT that cand perform such a task ?I am in the process of adding morphological analysis to IT, and one of =the measurements that will be provided is major and minor axis length.  =Although there will not be a plug-in which specifically computes the =smallest diameter, just having IT provide the diameter of all cells in =an image would be a good start.  The new version of IT should be =available some time in the next couple of weeks, I am tracking down the =last few bugs in the measurement routines.Many thanks in advance,Thank you for your interest in IT.Don Wilcox------------------------------End of IT-LIST Digest 1***********************