Hi Eric,
I have written some macros that split the Biorad dual-channel
split-image files; also one that does split-image Z-stacks. These are
basically modifications to the "Biorad Reader" plugin with some code
added to do the task at hand.
I would be happy to send or put the java and class files on my website
for download.
Below is an example for a single frame dual image. The others are longer.
/* Author: Dale A. Callaham
* email: [log in to unmask]
*
* Splits an OPEN (!) 2-channel Biorad Mrc-600 confocal image into the "Red"
* and "Green" channels. Assumes 768x512 dual-channel (side-by-side) image.
*
*/
import ij.*;
import ij.process.*;
import ij.gui.*;
import java.awt.*;
import ij.plugin.*;
public class BioRad_Splitter implements PlugIn {
public void run(String arg) {
IJ.run("Rename...", "title=Untitled");
IJ.selectWindow("Untitled");
IJ.makeRectangle(0, 0, 383, 511);
IJ.run("Copy");
IJ.run("New...", "name=Green type='8-bit Unsigned' fill=Black
width=384 height=512 slices=1");
IJ.run("Paste");
IJ.run("Select None");
IJ.selectWindow("Untitled");
IJ.makeRectangle(384, 0, 767, 511);
IJ.run("Copy");
IJ.run("New...", "name=Red type='8-bit Unsigned' fill=Black width=384
height=512 slices=1");
IJ.run("Paste");
IJ.run("Select None");
IJ.selectWindow("Untitled");
IJ.run("Select None");
}
}
##########################################
Eric Scarfone wrote:
> hej
> For a totally free software , CAS worked surprisingly well!
> It was particularly usefull to split and merge the infamous original
> Biorad split image format! To my knowledge it is the only software able
> to do that, even on stacks that can then be saved as tiff series.
> Brings back good mems!
>
> Eric
>
> Eric Scarfone, PhD, CNRS,
> Center for Hearing and communication Research
> Department of Clinical Neuroscience
> Karolinska Institutet
>
> Postal Address:
> CFH, M1:02
> Karolinska Hospital,
> SE-171 76 Stockholm, Sweden
>
> Work: +46 (0)8-517 79343,
> Cell: +46 (0)70 888 2352
> Fax: +46 (0)8-301876
>
> email: [log in to unmask]
> http://www.ki.se/cfh/
>
>
> ----- Original Message -----
> From: Guy Cox <[log in to unmask]>
> Date: Thursday, April 23, 2009 6:52 am
> Subject: Re: What open-source software did you use in the past and would
> like to use again?
> To: [log in to unmask]
>
> > Todd Brelje, not Berlji!
> >
> > According to the grapevine, he was working on a later version
> > which would work under NT and have an interface more like the
> > later Biorad software. (For those who don't know, Todd also wrote
> > the first version of COMOS, then called CM). However Bio-Rad
> > refused to allow him to continue with it, for unfathomable reasons
> > of their own. Since he had been given access to Bio-Rad source
> > code and had signed the appropriate agreements, he had no option
> > but to comply.
> >
> > Maybe someone else out there knows more details.
> >
> > Guy
> >
> >
> >
> > Optical Imaging Techniques in Cell Biology
> > by Guy Cox CRC Press / Taylor & Francis
> > http://www.guycox.com/optical.htm
> > ______________________________________________
> > Associate Professor Guy Cox, MA, DPhil(Oxon)
> > Electron Microscope Unit, Madsen Building F09,
> > University of Sydney, NSW 2006
> > ______________________________________________
> > Phone +61 2 9351 3176 Fax +61 2 9351 7682
> > Mobile 0413 281 861
> > ______________________________________________
> > http://www.guycox.net
> > -----Original Message-----
> > From: Confocal Microscopy List
> > [mailto:[log in to unmask]] On Behalf Of Dale Callaham
> > Sent: Thursday, 23 April 2009 1:20 PM
> > To: [log in to unmask]
> > Subject: Re: What open-source software did you use in the past and
> > would like to use again?
> >
> > Confocal Assistant was very nice for Biorad files in particular
> > and the things we tended to do with those images and stacks. But
> > in addition to the 8+3 filename limitation it seemed to also have
> > a restricted space allocated for the full path and filename string
> > and if files were more than a few directories deep with typical
> > names it seemed to fail to open the files - would show them in the
> > browser but couldn't open; if the files were simply moved closer
> > to the root level, it opened them fine.
> >
> > Dale
> >
> > Tina Carvalho wrote:
> > > Hey, that was what I was going to say! Confocal Assistant.
> > Really
> > > liked it. Hated the short file names.
> > >
> > > Aloha,
> > > Tina
> > >
> > >> Confocal Assistant by Todd Berlji would fall into this
> > category. It
> > >> was developed for Win 3.1, had a nice GUI and was very popular.
> > It
> > >> will run uder XP but only supports short file names. You can
> > download a copy at:
> > >> http://www.ludwig.edu.au/confocal/Links.html
> > >>
> > >> Cheers
> > >> Stephen Cody
> > >>
> > >> 2009/4/23 Cory Quammen <[log in to unmask]>
> > >>
> > >>> Dear list,
> > >>>
> > >>> Open-source and freely available software such as ImageJ, the
> > Open
> > >>> Microscopy Environment, and Micro-Manager are examples of
> > popular,
> > >>> actively-developed, and well-supported applications used
> > within the
> > >>> microscopy community. Presumably other popular software tools
> > useful
> > >>> in microscopy and image analysis have been created in the
> > past, but
> > >>> are no longer developed or supported because the original
> > >>> development team lacks funding or interest. My question for
> > the list is:
> > >>>
> > >>> What abandoned or neglected microscopy and image
> > analysis/processing
> > >>> software have you used in the past and would love to use again
> > if it
> > >>> were under active development, but currently do not use
> > because it
> > >>> either does not run or does not do something you want it to?
> > By
> > >>> active development, I mean that a team of developers would
> > release
> > >>> updated versions of the software from time to time with new
> > features
> > >>> and bug fixes.
> > >>>
> > >>> Thanks for your feedback,
> > >>> Cory
> > >>>
> > >>> --
> > >>> Cory Quammen
> > >>> Center for Computer Integrated Systems for Microscopy and
> > >>> Manipulation
> > >>> (CISMM)
> > >>> Department of Computer Science
> > >>> University of North Carolina at Chapel Hill
> > >>> http://www.cs.unc.edu/~cquammen
> > >>>
> > >
> > >
> >
> ****************************************************************************>
> * Tina (Weatherby) Carvalho * [log in to unmask] *
> > > * Biological Electron Microscope Facility * (808) 956-6251
> > *
> > > * University of Hawaii at Manoa *
> > http://www.pbrc.hawaii.edu/bemf*
> > >
> >
> **********************************************************************>
> ******
> >
> > No virus found in this incoming message.
> > Checked by AVG.
> > Version: 7.5.557 / Virus Database: 270.12.3/2075 - Release Date:
> > 22/04/2009 5:25 PM
> >
> >
> > No virus found in this outgoing message.
> > Checked by AVG.
> > Version: 7.5.557 / Virus Database: 270.12.3/2075 - Release Date:
> > 22/04/2009 5:25 PM
> >
> >
>
|
