http://imagej.273.s1.nabble.com/importing-LSM-files-into-ImageJ-and-losing-1-channel-tp3684595p3684597.html
really long acquisition times => 40 minutes per image. By doing the 2
Holly L. Aaron
> Hi Holly.
>
>
> On May 13, 2011, at 6:00 AM, IMAGEJ automatic digest system wrote:
>
> >
> > Date: Thu, 12 May 2011 14:43:13 -0700
> > From: Holly Aaron <
[hidden email]>
> > Subject: importing .LSM files into ImageJ and losing 1 channel
> >
> > Dear ImageJ Community - Hello! It has been a long time since I've been on
> > the list. I am happy to see it is still so active!
> >
> > Anyway, one of my users recently ran into an unusual problem with
> importing
> > files from the Zeiss 710 Zen software. She is doing large tile scans
> (6x8
> > or bigger) z-stacks (20+ z- planes), so the files are 0.5G++. She is
> doing
> > them in 2 rounds to get 3 colors w/o any cross-talk: first GFP & Cy5 and
> > then Cy3. She then adds the Cy3 channel to the other image to create a
> > 3-channel image.
>
> this is not the optimal way.
>
> you should use 2 different "tracks"
> 1st track has GFP and Cy5
> and the second track has Cy3.
>
> then all the images get saved into the same .lsm file from the get go.
>
> Imaging twice then merging the 2 files is an inefficient an derror prone
> way to do it.
>
>
> > She's saving in the .lsm format. All the data (all 3
> > channels) are there if she re-opens in Zen. But when she imports the file
> > into ImageJ, there are only the first 2 channels.
>
> the most versatile way to open .lsm file
> is probably the bio-formats importer plugin , part of the LOCI toos
> package.
>
> If you use Fiji, ist already bundled and up to date and found in
> plugins - loci - bio-formats importer
>
> there is also the LSM toolbox plugins set.
>
>
> > Does anyone know what
> > could be happening to the 3rd channel? Are there limits to the file
> sizes
> > that can be opened?
>
> No, there is no limit... only in the RAM your computer....
> and if that gets full, the java virtual machine running imageJ will
> complain loudly to you
> via a nice error message.
>
> I strongly sugest you use 2 or 3 "tracks"
> in the Zen aodtware to do the imaging.
>
> this works great for us and many others.
>
> you can so a multi track (multi channel), z stack, tile scan, time series
> even ....
> and alll gets saved in one huge .lsm file...
>
> cheers
>
> dan
>
>
>
> >
> > Thanks for any advice or help!
> >
> > -Holly
> > ___________________________
> > Holly L. Aaron
> > Molecular Imaging Center
> > Cancer Research Laboratory
> > University of California Berkeley
> > 251 LSA #2751
> > Berkeley, CA 94720-2751
> > 510.642.2901
> > 510.642.5741 fax
> >
[hidden email]
> >
http://imaging.berkeley.edu>
> Dr. Daniel James White BSc. (Hons.) PhD
> Senior Microscopist / Image Visualisation, Processing and Analysis
> Light Microscopy and Image Processing Facilities
> Max Planck Institute of Molecular Cell Biology and Genetics
> Pfotenhauerstrasse 108
> 01307 DRESDEN
> Germany
>
> +49 (0)15114966933 (German Mobile)
> +49 (0)351 210 2627 (Work phone at MPI-CBG)
> +49 (0)351 210 1078 (Fax MPI-CBG LMF)
>
>
http://www.bioimagexd.net BioImageXD
>
http://pacific.mpi-cbg.de Fiji - is just ImageJ (Batteries
> Included)
>
http://www.chalkie.org.uk Dan's Homepages
>
https://ifn.mpi-cbg.de Dresden Imaging Facility Network
> dan (at) chalkie.org.uk
> ( white (at) mpi-cbg.de )
>
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