Nikon EZ C1 advice

[Michael Bastiani]

We just started working with Nikon EZC1 and noted some issues that others might have
already dealt with.  
1. Is there any way to adjust the Z position during a time lapse experiment without ending
the experiment and starting a new one?
2.  Time lapse experiments are saved as z-stacks for each time point.  Is there an imageJ
plug in or does someone have a macro that will convert each time point z-stack to a
maximum projection and then assemble into a movie?  
3.  EZC1 generates avi movies that I can not open on my Mac (OS10.6.2) even though I
have installed the Flip4mac plugin.  The only program that will open the avi is imageJ.  I
have also tried Handbrake and VisualHub. Neither one will recognize the avi movies
generated by EZC1.  However, any avi movie that I download from the web is recognized
and plays just fine by all Mac programs.  
4.  When taking a z-stack there seems to be an inordinate time spent doing nothing
between each z step before scanning.  The Nikon reps say that this is to allow "settling" of
the speciman/stage so that vibrations do not degrade the image.  Is there anyway to adjust
the wait or settling time between scans?
5.  Anyone have any idea if Nikon will ever "port" Elements to the C1?
6.  Has anyone attempted to control the C1 with open source software?

[Craig Brideau]

> We just started working with Nikon EZC1 and noted some issues that others might have
> already dealt with.
> 1. Is there any way to adjust the Z position during a time lapse experiment without ending
> the experiment and starting a new one?

First a question: What version of EZC1 are you using?  Now some answers:
No, the time lapse function just keeps doing the same volume every
time point.  If your stage or sample is not stable you will have
problems.  On the other hand, Nikon does have a pretty good autofocus
module that can be attached to certain models.  If your sample is
drifting out of your imaged volume over time this might help keep it
in view.

> 2.  Time lapse experiments are saved as z-stacks for each time point.  Is there an imageJ
> plug in or does someone have a macro that will convert each time point z-stack to a
> maximum projection and then assemble into a movie?
> 3.  EZC1 generates avi movies that I can not open on my Mac (OS10.6.2) even though I
> have installed the Flip4mac plugin.  The only program that will open the avi is imageJ.  I
> have also tried Handbrake and VisualHub. Neither one will recognize the avi movies
> generated by EZC1.  However, any avi movie that I download from the web is recognized
> and plays just fine by all Mac programs.

I strongly suggest you try out our freeware software called ImageTrak.
 It runs on Mac only and is specifically designed to process Nikon
ics/ids files.  You can get it from our lab's website:
http://www.ucalgary.ca/styslab/imagetrak
It doesn't do movies but it will do MIPs.  It also exports to Osirix
(another free/low cost app) which you can then use to make movies.

> 4.  When taking a z-stack there seems to be an inordinate time spent doing nothing
> between each z step before scanning.  The Nikon reps say that this is to allow "settling" of
> the speciman/stage so that vibrations do not degrade the image.  Is there anyway to adjust
> the wait or settling time between scans?

I was under the impression that this was the stage moving back to the
top of the stack.  I don't notice much wait time.

> 5.  Anyone have any idea if Nikon will ever "port" Elements to the C1?

There were rumors a while back, and Elements will partially run the
C1Si currently, but I don't think they are putting much effort into it
at the moment.

> 6.  Has anyone attempted to control the C1 with open source software?

I looked into it, but you would have to work out all the different
control signals.  We actually stuck with EZC1 after looking at all the
effort it would take to write our own control software.

Craig Brideau
Hotchkiss Brain Institute
University of Calgary