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Hi Christian,

You can save a lot of time by automating steps in ImageJ by writing macros for recurring tasks like "import nd2->split channels->merge two channels>save as tiff".
Let me know if you need sample code or do a quick web search. There are a lot of macro examples on the web.
There is also the batch process option in Fiji under Process->Batch->

Hope that helps!

Jens 


On Jun 17, 2014, at 2:10 PM, Christian <[log in to unmask]> wrote:

> I am employed in a very diverse multi-user core facility.  
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
> 
> Listers,
> 
> I am employed in a very diverse multi-user core facility.  I primarily operate the Nikon A1 between 5 and 7 hours a day for a wide range of users, from undergraduates to PI's.  In any case, the issue I have is that exporting or minor edits to the raw .nd2 files must occur on the A1 system as our users are mostly completely ignorant and we have no imaging software which is not dedicated to a system.  It's amazing how much time I lose trying to export a two channel z-projection from a three channel .nd2.  Do any of you have any suggest software or tutorials I might build upon to provide to my users?  Nearly everything we do is supplementary information (figures), not quantitative, but then I do not believe the users know the difference between an .nd2 and a .jpg.  
> 
> I have used the FIJI build of ImageJ for some users, but getting folks trained up is also time consuming.  I understand I may be out of luck in this venture.  I do thank you for any help you might provide.
> 
> Christian