Date: Fri, 19 Aug 1994 08:58:41 +0100 Subject: Re: Ooops - forgot the generic info To: thorpe@mcnc.org X-Fax-Defaults: /STN=+49 6221 387 0/SFN=+49 6221 387 306 X-Vms-To: IN%"thorpe@mcnc.org" Hi Steve, Thanks for the reply! If you think that the slicer is OK then you can certainly put it out on the public domain site. It would be interesting to hear comments from other people. My boss comes back from 3weeks holiday/work on Monday, so hopefully we can get things moving again with this article. And in the meantime I am trying to get my reader module to work on SGI.... I wonder if you have any suggestion. I have a motiv interface which handles drawing and stuff in a window. It works on DEC, but on the SGI the root window (from which my window takes most of its attributes) is only 8bit and not 24 or 32. Do you know how avs handles this? I know that to configure my avs setup on the machine I have to set the VisualID parameter in the .avsrc file, but what is avs actually doing with this? (Don't worry if this is a ridiculously specific question, I am sure I will suss it somehow before the day/week/year is out!) All the best - Nick From: Nick Salmon Subject: confocal slicer To: thorpe@mcnc.org Status: RO Hi Steve, You may remember that I promised you an article for AVS network news some time ago. Well.... Since then I wrote something about what I've been doing with AVS, but my boss is keen to get it published in a traditional scientific journal :-( Reasoning for this is that the data for the images which I wanted to show has not yet been published in a scientific journal, and such critically reviewed work is worth more points when we write our lab report at the end of the year. Whether an obscure journal is more use to humankind I don't know. Anyway, no doubt it will be a trivial task to edit and submit something to you (if nobody else does first!) when we get rid of what I already wrote. Sorry about this. Anyway, writing something did focus me a bit more on the strengths and weaknesses of AVS, such that I wrote a few modules, one of which is probably OK for you to try out if you like. An enormous number of confocal experiments yeild data with two channels (i.e. two fluorescent dyes in the same specimen). What one usually does is to assign one dye to say red, and the other dye to green in a 3D 4-vector field. Then I want to slice it.....Easier said than done. So I wrote a module which is basically it's a hack on the "new arbitrary slicer". The main features of it are covered in the help file, and no doubt you can work out the problems you would have doing the same thing with other modules. You can pick up the module via anonymous ftp from: tom.embl-heidelberg.de /confocal_slicer There is also an example data set there for your own private playing about! I hope that this is of interest to you, and also that I will eventually be able to submit something for the magazine. Perhaps you could inform me of when the submission dates are? All the best, Nick Salmon Light Microscopy Group European Molecular Biology Laboratory Meyerhofstrasse 1 69117 Heidelberg Tel: +49 6221 387 354 Fax: +49 6221 387 306 email: salmon@EMBL-Heidelberg.DE