http://imagej.273.s1.nabble.com/Adjust-image-filters-with-TraKEM2-tp5015635p5015645.html
> Seeing this is the 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
> Glad to hear. I assume that you mean RAM usage as reported by some
> system administration tool (top, task manager?)? Seeing this is the
> 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
> to observe the 'real' memory usage of Fiji/ TrakEM2, use a JVM monitor
> such as jvisualvm. There are anumber of threads covering this in the
> mailing list and forum.
>
> Cheers,
> Stephan
>
>
> On Mon, 2016-02-15 at 23:37 +0100, Federico Luzzati wrote:
> > 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> > >
> >
> >
> >
>
> --
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