Re: Adjust image filters with TraKEM2

Posted by Saalfeld, Stephan on Feb 15, 2016; 5:12pm
URL: http://imagej.273.s1.nabble.com/Adjust-image-filters-with-TraKEM2-tp5015635p5015639.html

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
>

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