<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><BR><DIV><BR><DIV>Begin forwarded message:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><B>From: </B></FONT><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">"#HU GUANGHUI#" <<A href="mailto:S8118235C@ntu.edu.sg">S8118235C@ntu.edu.sg</A>></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><B>Date: </B></FONT><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">May 31, 2006 12:03:31 PM BDT</FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><B>To: </B></FONT><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">"Tom Macura" <<A href="mailto:tm289@cam.ac.uk">tm289@cam.ac.uk</A>></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><B>Subject: </B></FONT><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><B>RE: Matlab Integration with OME</B></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> <BR><P><FONT size="2">Hi Tom,<BR> <BR> Thanks for pointing out the error I've made.<BR> <BR> After installing of the perl modules needed by OME, clean up my OME database, everything is running smoothly (or at least that's what i think). During the installation, at some point the program displayed something like:<BR> <BR> Xlib: No protocol specified<BR> <BR> Xlib: connection to ":0.0" refused by server<BR> Xlib: No protocol specified<BR> <BR> [SUCCESS]<BR> <BR> I dont really know what it means but I'm hoping the "[SUCCESS]" should indicate everything is still installed properly.<BR> <BR> So if the installation was successful, I guess the next thing is to test Matlab proper. From OME's website, there's this HistogramEqualizationChain.xml as well as the module that can be used for testing, however, i think i'm stuck again.<BR> <BR> Questions start to appear over my head, should i first import analysis chain or module or both?<BR> Also, from the instructions, am i right to say that in the Matlab R12 and above there's a function/command called "histeq"? And in order to use this function i need to first import into OME and then execute this function on the datasets in OME?<BR> <BR> Based on my assumption that the flow is what described above, would there be any difference when it comes to user-defined functions? Is it for every function to be used, a analysis chain and module is to be created? If so, is there a standard way to create them?<BR> <BR> Thank you once again!<BR> <BR> Cheers,<BR> GuangHui<BR> <BR> -----Original Message-----<BR> From: Tom Macura [<A href="mailto:tm289@cam.ac.uk">mailto:tm289@cam.ac.uk</A>]<BR> Sent: Wed 5/31/2006 12:39 AM<BR> To: #HU GUANGHUI#<BR> Cc: ome-devel Development<BR> Subject: Re: Matlab Integration with OME<BR> <BR> Hi,<BR> <BR> You did almost everything right.<BR> <BR> A CVS checkout basically is equivalent to an OME install package. You <BR> have to install OME (by running perl install.pl)<BR> even after checkout.<BR> <BR> So you have to check out into your home directory. e.g. /home/tmacur1 <BR> or /home/guanghui<BR> instead of / as you currently did.<BR> <BR> Then you have to install by running sudo perl /home/tmacur1/OME/<BR> install.pl<BR> <BR> so now do<BR> <BR> rm -rf /OME (To remove your current OME checkout -- it's in the wrong <BR> place)<BR> cd /home/guanghui (to move to your home directory)<BR> cvs -z3 -d ':pserver:<A href="mailto:anoncvs@cvs.openmicroscopy.org.uk">anoncvs@cvs.openmicroscopy.org.uk</A>:/ome' checkout <BR> OME (to do a current checkout)<BR> cd OME<BR> sudo perl install.pl (to install OME).<BR> <BR> Let me know if you need more info or have further questions,<BR> <BR> Tom<BR> <BR> <BR> On May 30, 2006, at 5:13 PM, #HU GUANGHUI# wrote:<BR> <BR> ><BR> > Hi Tom,<BR> ><BR> > Thanks for the quick reply!<BR> ><BR> > As it is my first time using cvs, this is what i've done.<BR> > (I'm using fedora core 3 in case the platform matters)<BR> > As the root, under the "/" directory, i ran these commands:<BR> ><BR> > $ cvs -d ':pserver:<A href="mailto:anoncvs@cvs.openmicroscopy.org.uk">anoncvs@cvs.openmicroscopy.org.uk</A>:/ome' login<BR> > CVS password:anoncvs<BR> > $ cvs -z3 -d ':pserver:<A href="mailto:anoncvs@cvs.openmicroscopy.org.uk">anoncvs@cvs.openmicroscopy.org.uk</A>:/ome' <BR> > checkout OME<BR> ><BR> > Then the cvs did a lot of updating and checkout.<BR> ><BR> > Next I ran this, under "/OME" the directory where OME is installed<BR> > $ cvs update -d<BR> ><BR> > However, i saw warning messages like the following<BR> ><BR> > cvs update: Updating conf<BR> > cvs update: warning: cannot write history file /ome/CVSROOT/<BR> > history: Permission denied<BR> > cvs update: move away conf/httpd.ome.conf; it is in the way<BR> > C conf/httpd.ome.conf<BR> > cvs update: warning: cannot write history file /ome/CVSROOT/<BR> > history: Permission denied<BR> > cvs update: move away conf/httpd.omeds-dev.conf; it is in the way<BR> > C conf/httpd.ome.conf<BR> ><BR> > and the list goes on...<BR> > And when i did a "slocate CVSROOT", it was not able to find such <BR> > directory.<BR> > So I was afraid I did something wrong, or misunderstand the <BR> > instructions.<BR> ><BR> > Also, I understand OME can be "reinstalled" if so how am I going to <BR> > perform the reinstallation?<BR> > Is it by running the script "install.pl" that is found in the <BR> > directory of the installed OME?<BR> ><BR> > Thanks for your time, I'm also eager to get the integration up and <BR> > running.<BR> ><BR> > Cheers,<BR> > GuangHui<BR> ><BR> > -----Original Message-----<BR> > From: Tom Macura [<A href="mailto:tm289@cam.ac.uk">mailto:tm289@cam.ac.uk</A>]<BR> > Sent: Sun 5/28/2006 3:24 AM<BR> > To: #HU GUANGHUI#<BR> > Subject: Re: Matlab Integration with OME<BR> ><BR> > Hi GuangHui,<BR> ><BR> > If you want to use OME with MATLAB you really have no choice but to<BR> > get the latest version of OME from CVS (info at<BR> > cvs.openmicroscopy.org.uk).<BR> > The current release (2.4.0) is over a year old. There have been many<BR> > many improvements to the OME/MATLAB coupling. A new release is in<BR> > the pipeline but I have no idea when it will happen.<BR> ><BR> > The CVS version of OME is pretty good -- don't worry about bugs the<BR> > MATLAB part is very thoroughly tested (because we use it all the time<BR> > as infrastructure for our own research) Unfortunately they are always<BR> > unknown problems.<BR> ><BR> > You might want to look at the paper I wrote about OME/MATLAB<BR> > coupling: <A href="http://www.openmicroscopy.org.uk/publications/">http://www.openmicroscopy.org.uk/publications/</A><BR> > MatlabHandler.pdf<BR> ><BR> > Hope things work for you. Don't hesitate to write back. I'm very<BR> > excited you're interested in OME+MATLAB and want to help you,<BR> ><BR> > Best,<BR> ><BR> > Tom<BR> ><BR> <BR> <BR> </FONT> </P> </BLOCKQUOTE></DIV><BR></BODY></HTML>