Re: importing .LSM files into ImageJ and losing 1 channel

Posted by Daniel James White on May 13, 2011; 8:57am
URL: http://imagej.273.s1.nabble.com/importing-LSM-files-into-ImageJ-and-losing-1-channel-tp3684595p3684596.html

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

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (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 )