How to save a file in LSM format in ImageJ?

[mia2005]

Hello all,
 
I am acquiring my Zstack images with a Leica LSM710 using the program ZEN
that saves the images in LSM format. Then I want to measure co-localization
of 2 out of my 4 channes with IMARIS.
However, prior to my analysis in IMARIS, I would like to edit them in ImageJ
to delete some areas (by using edit>clear selection, I can delete the
nucleus out of my analysis plane for example). However, after I do this, I
am not able to save this file in a format that I can open it in IMARIS. I
tried several formats, and the ones that do open something, only one channel
shows up instead of the 4.
Does anyone know how to do this?
 
Thank you very much

[ctrueden]

Hi,

> I am not able to save this file in a format that I can open it in
> IMARIS. I tried several formats, and the ones that do open something,
> only one channel shows up instead of the 4.

I advise you not to resave in a proprietary file format like Zeiss LSM. Use
an open file format such as OME-TIFF. The Bio-Formats Exporter plugin for
ImageJ (bundled with Fiji) can save as OME-TIFF.

Imaris can open OME-TIFF files [1]. If you have problems, you can report
them to Bitplane.

Alternately, Imaris also has integration with Fiji [2], which could allow
you to perform your ImageJ-based workflow directly from within Imaris.

Regards,
Curtis

[1] http://www.bitplane.com/go/products/imaris, "Datasheet" tab, "Supported
formats" section
[2]
http://www.bitplane.com/go/knowledge-base/how-to--/enabling-imagej/fiji-and-matlab-plugins-in-imaris

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[hardtofind]

I want to crop an LSM and save it in the same LSM format, even if that isn't optimal for many workflows.  So, the question remains... is it possible to save LSM from ImageJ?  Many thanks,
Hardy