[OpenSPIM] Fiji/Micromanager conflicts

[Monika Pawłowska]

Hi,

just for your information - just now the strategy of using  
Fiji+Micro-manager-dev+Openspim is not perfect. The Micro-manager-dev  
update site is not updating since 30.04., and this version has some  
conflicts with the newest version of Fiji, so there might be errors. Below  
the response I got from Micromanager that hopefully explains this better.

(I found about this because I tried to use the Micro-Manager  
Multi-Dimensional Acquisition and I was getting an exception when trying  
to save a stack).

Regards,
Monika





------- Treść oryginalnej wiadomości -------
Od: "Mark Tsuchida" <marktsuchida at gmail.com>
Do: "Chris Weisiger" <cweisiger at msg.ucsf.edu>
Kopia dla: m.pawlowska at nencki.gov.pl, "info at micro-manager.org  
micromanager" <info at micro-manager.org>
Temat: Re: New Problem Report: 2015-05-13 Monika Pawlowska
Data: środa, .05.2015,

Hi Monika,

On Wed, May 13, 2015 at 09:38:21AM -0700, Chris Weisiger wrote:
> On Wed, May 13, 2015 at 9:15 AM, <m.pawlowska at nencki.gov.pl> wrote:
> > W dniu 2015-05-13 17:52, Chris Weisiger napisał(a):
> > indeed, with the newest nightly build the acquisition works. But this
> > solves my problem only partly. I am normally using fiji with  
> Micromanager
> > update site, and from there the newest build is the 20150430, this is  
> why
> > I'm using this version. I would prefer to use fiji to have all the
> > aditional functionality. Is there any chance to get the update site
> > updated, so to say?
>
> Okay, good to know we've at least narrowed down what's going on. In this
> case I suspect the actual problem isn't the version of Micro-Manager, but
> the version of the OME library in Fiji. Sometimes Micro-Manager and Fiji
> depend on the same library, but require different versions of that  
> library,
> which is unfortunate; we're trying to resolve such issues when we  
> discover
> them.
>
> In the meantime, you can try replacing the library manually. This is a  
> jar
> file called "ome-xml.jar", which should be in the "plugins/Micro-Manager"
> directory of the nightly download. You can try just replacing the
> corresponding .jar file in your Fiji installation with the one from the
> nightly build. Make a backup of the original .jar file though, just in  
> case
> something else in Fiji breaks. In the meantime, we can look into what it
> would take to get the update site updated.

The conflict is in other JARs. We still use an outdated version of
scifio.jar, which conflicts with the newer version in Fiji. We fully
intend to fix this, and it will hopefully not be too hard, but it is not
trivial (we need to make sure we don't introduce issues into file saving
in our official release, and that will require careful testing).

Please consider the Micro-Manager-dev update site to be experimental.

I don't think there is an easy fix at this moment that can be done by
just replacing JARs. We'll keep working on it!

Best,
Mark


-- 
Dr Monika Pawłowska
Nencki Institute
Laboratory of Neurobiology
3, Pasteur Street
02-093 Warsaw, Poland
phone: (+48) 22 5892 427