Fail to modify channel opacity in TrakEM2

[Federico Luzzati]

Hi,
My name is Federico Luzzati and I'm trying to use TrakEM2 to align and reconstruct confocal stacks from serial sections.

I have two main problems:

1) I'm using RGB images,  but in  the opacity tab I cannot hide channels neither by unchecking the box  or using the slider, I also tryed with RGB stacks, and different files formats (TIF/Jpeg) but nothing changed. I was also wondering whether channels opacity may apply only to the selected layer, or to the entire reconstruction (something that would be really useful for me)

2) I'd like to perform reconstructions using stacks with multiple channels, (actually "only" four). Any suggestions on how to add a fourth channel? I saw some composite options right clicking in the layer, but could not find them mentioned on the manual.

Thanks a lot for any help

Federico

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[Stephan Saalfeld]

Hi Federico,

TrakEM2's multi-channel support is a bit convoluted, however flexible in
the way how you can use it.  While it supports RGB images and stacks,
you have little control there what to do with the channels.  The better
option is to separate your images stack into single channel images with
a distinct name (such as "blabla-red.tif") and import them individually
into the same project.  You can now adjust the channels individually:

Selection->Select all that match...

e.g. Start: 1, End: 1000, Regular expression: .*red.*

Adjust Images->Adjust image filters (selected images)

LUTRed

Properties...
Composite mode: Add

You'll get it...

The alignment procedures will work on a gray-projection of the
contrast-overlay setup that you see on screen.  This way you can
experiment with settings that perform best for alignment (rich texture)
and later change them to what seems optimal for annotation (clear
separable signal).

Good luck and best regards,
Stephan

PS. While the described [procedure should in principle work, I noticed
that they currently do not because of two bugs in TrakEM2:

http://fiji.sc/cgi-bin/bugzilla/show_bug.cgi?id=435

http://fiji.sc/cgi-bin/bugzilla/show_bug.cgi?id=436

Hope that they turn out to be easy to fix.  Keeping you posted...





On Mon, 2012-06-11 at 03:00 -0400, Federico Luzzati wrote:

> Hi,
> My name is Federico Luzzati and I'm trying to use TrakEM2 to align and
> reconstruct confocal stacks from serial sections.
>
> I have two main problems:
>
> 1) I'm using RGB images, but in the opacity tab I cannot hide channels
> neither by unchecking the box or using the slider, I also tryed with
> RGB stacks, and different files formats (TIF/Jpeg) but nothing
> changed. I was also wondering whether channels opacity may apply only
> to the selected layer, or to the entire reconstruction (something that
> would be really useful for me)
>
> 2) I'd like to perform reconstructions using stacks with multiple
> channels, (actually "only" four). Any suggestions on how to add a
> fourth channel? I saw some composite options right clicking in the
> layer, but could not find them mentioned on the manual.
>
> Thanks a lot for any help
>
> Federico
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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