http://imagej.273.s1.nabble.com/Adjust-image-filters-with-TraKEM2-tp5015635p5015644.html
Glad to hear. I assume that you mean RAM usage as reported by some
typical behavior of the JVM, i.e. all Java/Scala/Groovy/...
applications. You can limit the amount of memory used by the JVM using
the -Xmx parameter. But you will keep seeing JVM memory usage to
approach this limit and then stay there for its lifetime. If you want
such as jvisualvm. There are anumber of threads covering this in the
> Thank you Stephan and Albert,
> the type="3" trick magically solved the problem! The RAM still tend
> to
> accumulate in a strange way (altough I never run out of memory), but
> this
> seem rather a general problem of fiji, not specifically of TraKEM2,
> indeed
> the script suggested by Albert have no effect in my system.
> Thank you very much!
>
> Federico
>
> 2016-02-15 18:23 GMT+01:00 Saalfeld, Stephan <
>
[hidden email]>:
>
> > I confirm it's a bug. I will see what I can do over the next days
> > but
> > may not have enough time to get into this. If you love the risky
> > life
> > (you use Fiji and TrakEM2, so you do!), you can get it to work
> > right
> > now by editing the project XML file.
> >
> > In the XML, you will find a property
> >
> > type="0"
> >
> > for each 8-bit
> >
> > <t2_patch ...>
> >
> > entry (the tiles). If you replace this by
> >
> > type="3"
> >
> > TrakEM2 seems to be sufficiently convinced that these are color
> > images
> > to render them with the LUT. In vim, the correct global replace
> > command is
> >
> > :%s/type="0"/type="3"/g
> >
> > I have tested this only on a small set of images and it may have
> > unintended side effects, so you should probably do this in a copy
> > of
> > your XML file.
> >
> > Let me know.
> >
> > Best,
> > Stephan
> >
> >
> > On Mon, 2016-02-15 at 15:29 +0100, Federico Luzzati wrote:
> > > Dear List,
> > > I'm using TrakEM2 to reconstruct bundles of nerve fibers from
> > > four
> > > channels
> > > confocal images ( a huge serial section reconstruction). As
> > > suggested
> > > by
> > > Stephan Saalfeld (some yeras ago!) I imported the channels as
> > > separate
> > > 8-bit patches, applyed a LUT with "adjust image filters" and set
> > > the
> > > composite mode to Add. However if I close and re-open the project
> > > the
> > > color
> > > of the LUTs turns to gray and I have to set everithing again and
> > > wait
> > > the
> > > (long) regeneration of the minimaps. Moreover, since the RAM is
> > > apparently
> > > not released after the process (running the garbage collector is
> > > ineffective) scrolling through the sections for annotation become
> > > very
> > > slow. Is this a bug? Are there alterantive ways to change the LUT
> > > of
> > > the
> > > channels?
> > >
> > > Thank you
> > >
> > > Federico
> > >
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
>
>
>