Re: Adjust image filters with TraKEM2

Posted by Albert Cardona-2 on Feb 15, 2016; 7:12pm
URL: http://imagej.273.s1.nabble.com/Adjust-image-filters-with-TraKEM2-tp5015635p5015641.html

Dear Federico,

About the memory build up: in some systems, TrakEM2 mipmaps accumulate in
the internal cache beyond what would be optimal. To release them, run the
following from e.g. a jython interpreter:

from ini.trakem2 import Project
Project.getProjects()[0].getLoader().releaseAll()


The above can run as well from a ScheduledService every minute if
necessary. For example, from the interpreter run this:

###
from java.util.concurrent import Executors, TimeUnit

def releaseAll():
  Project.getProjects()[0].getLoader().releaseAll()

exe = Executors.newSingleThreadScheduledExecutor()
exe.scheduleAtFixedRate(releaseAll, 0, 60, TimeUnit.SECONDS)
###

To stop it, type:

exe.shutdown()


Hope this helps.

Albert Cardona



2016-02-15 9:29 GMT-05:00 Federico Luzzati <[hidden email]>:

> 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
>
> --
> Federico Luzzati, PhD
> Assistant Professor
> University of Turin,
> Dept. LIfe Sciences and Systems Biology (DBIOS)
> Via Accademia Albertina, 13 - 10123 Torino - IT
>
> Researcher at
> Neuroscience Institute Cavalieri Ottolenghi (NICO)
> Regione Gonzole, 10 - 10043 Orbassano (To) - IT
>
> tel. [phone]/ -6631
> http://www.nico.ottolenghi.unito.it/index.php/it/adult-neurogenesis
>
> Sostieni con il tuo 5xmille il NICO e la ricerca sulle malattie
> neurodegenerative
> Firma nel riquadro "Finanziamento della ricerca scientifica e
> dell'Università"
> CF 97564560015
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
http://albert.rierol.net
http://www.janelia.org/lab/cardona-lab
http://www.ini.uzh.ch/~acardona/

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